Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
161  structures 5079  species 3  interactions 10091  sequences 147  architectures

Family: ADK (PF00406)

Summary: Adenylate kinase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Adenylate kinase". More...

Adenylate kinase Edit Wikipedia article

Adenylate kinase
Adenylate kinase 2C95.png
3D ribbon/surface model of adenylate kinase in complex with bis(adenosine)tetraphosphate (ADP-ADP)
Identifiers
Symbol ADK
Pfam PF00406
InterPro IPR000850
PROSITE PDOC00104
SCOP 1ake
SUPERFAMILY 1ake

Adenylate kinase (EC 2.7.4.3) (also known as ADK or myokinase) is a phosphotransferase enzyme that catalyzes the interconversion of adenine nucleotides (ATP, ADP, and AMP). By constantly monitoring phosphate nucleotide levels inside the cell, ADK plays an important role in cellular energy homeostasis.

ADK_lid
PDB 1zip EBI.jpg
Bacillus stearothermophilus adenylate kinase
Identifiers
Symbol ADK_lid
Pfam PF05191
InterPro IPR007862
PROSITE PDOC00104
SCOP 1ake
SUPERFAMILY 1ake
Adenylate kinase
Identifiers
EC number 2.7.4.3
CAS number 2598011
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
PDB image 3HPQ showing the ADK enzyme skeleton in cartoon and the key residues as sticks and labeled according to their placement in E. Coli, crystallized with Ap5A inhibitor.

Substrate and Products

The reaction catalyzed is:

ATP + AMP ⇔ 2 ADP

The equilibrium constant varies with condition, but it is close to 1.[1] Thus, ΔGo for this reaction is close to zero. In muscle from a variety of species of vertebrates and invertebrates, the concentration of ATP is typically 7-10 times that of ADP, and usually greater than 100 times that of AMP.[2] The rate of oxidative phosphorylation is controlled by the availability of ADP. Thus, the mitochondrion attempts to keep ATP levels high due to the combined action of adenylate kinase and the controls on oxidative phosphorylation.

Isozymes

To date there have been nine human ADK protein isoforms identified. While some of these are ubiquitous throughout the body, some are localized into specific tissues. For example, ADK7 and ADK8 are both only found in the cytosol of cells; and ADK7 is found in skeletal muscle whereas ADK8 is not.[3] Not only do the locations of the various isoforms within the cell vary, but the binding of substrate to the enzyme and kinetics of the phosphoryl transfer are different as well. ADK1, the most abundant cytosolic ADK isozyme, has a Km about a thousand times higher than the Km of ADK7 and 8, indicating a much weaker binding of ADK1 to AMP.[4] Sub-cellular localization of the ADK enzymes is done by including a targeting sequence in the protein.[3] Each isoform also has different preference for NTP's. Some will only use ATP, whereas others will accept GTP, UTP, and CTP as the phosphoryl carrier.

Some of these isoforms prefer other NTP's entirely. There is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, that can only use GTP or ITP as the phosphoryl donor.[5] ADK has also been identified in different bacterial species and in yeast.[6] Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Some rfesidues are conserved across these isoforms, indicating how essential they are for catalysis. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.

Subfamilies

Mechanism

Phosphoryl transfer only occurs on closing of the 'open lid'. This causes an exclusion of water molecules that brings the substrates in proximity to each other,[7] lowering the energy barrier for the nucleophilic attack by the γ-phosphoryl group of ATP on the α-phosphoryl of AMP. In the crystal structure of the ADK enzyme from E. Coli with inhibitor Ap5A, the Arg88 residue binds the Ap5A at the α-phosphate group. It has been shown that the mutation R88G results in 99% loss of catalytic activity of this enzyme, suggesting that this residue is intimately involved in the phosphoryl transfer.[8] Another highly conserved residue is Arg119, which lies in the adenosine binding region of the ADK, and acts to sandwich the adenine in the active site. It has been suggested that the promiscuity of these enzymes in accepting other NTP's is due to this relatively inconsequential interactions of the base in the ATP binding pocket.[9] A network of positive, conserved residues (Lys13, Arg123, Arg156, and Arg167 in ADK from E. Coli) stabilize the buildup of negative charge on phosphoryl group during the transfer. Two distal aspartate residues bind to the arginine network, causing the enzyme to fold and reduces its flexibility. A magnesium cofactor is also required, essential for increasing the electrophilicity of the phosphate on AMP, though this magnesium ion is only held in the active pocket by electrostatic interactions and dissociates easily.[9]

Structure

Residues of ADKE. Coli involved in substrate binding

Flexibility and plasticity allow proteins to bind to ligands, form oligomers, aggregate, and perform mechanical work.[10] Large conformational changes in proteins play an important role in cellular signaling. Adenylate Kinase is a signal transducing protein; thus, the balance between conformations regulates protein activity. ADK has a locally unfolded state that becomes depopulated upon binding.[11]

Describes the generic kinetic cycle of the ADK enzyme family. Ternary complex is labeled.

A 2007 study by Whitford et al. shows the conformations of ADK when binding with ATP or AMP.[10] The study shows that there are three relevant conformations or structures of ADK—CORE, Open, and Closed. In ADK, there are two small domains called the LID and NMP.[12] ATP binds in the pocket formed by the LID and CORE domains. AMP binds in the pocket formed by the NMP and CORE domains. The Whitford study also reported findings that show that localized regions of a protein unfold during conformational transitions. This mechanism reduces the strain and enhances catalytic efficiency. Local unfolding is the result of competing strain energies in the protein.[10]

The local (thermodynamic) stability of the substrate-binding domains ATPlid and AMPlid has been shown to be significantly lower when compared with the CORE domain in ADKE. Coli.[13] Furthermore, it has been shown that the two subdomains (ATPlid and AMPlid) can fold and unfold in a "non-cooperative manner."[13] Binding of the substrates causes preference for 'closed' conformations amongst those that are sampled by ADK. These 'closed' conformations are hypothesized to help with removal of water from the active site to avoid wasteful hydrolysis of ATP in addition to helping optimize alignment of substrates for phosphoryl-transfer.[14] Furthermore, it has been shown that the apoenzyme will still sample the 'closed' conformations of the ATPlid and AMPlid domains in the absence of substrates.[7] When comparing the rate of opening of the enzyme (which allows for product release) and the rate of closing that accompanies substrate binding, closing was found to be the slower process.

Function

Metabolic Monitoring

The ability for a cell to dynamically measure energetic levels provides it with a method to monitor metabolic processes.[15] By continually monitoring and altering the levels of ATP and the other adenyl phosphates (ADP and AMP levels) adenylate kinase is an important regulator of energy expenditure at the cellular level.[16] As energy levels change under different metabolic stresses adenylate kinase is then able to generate AMP; which itself acts as a signaling molecule in further signaling cascades. This generated AMP can, for example, stimulate various AMP-dependent receptors such as those involved in glycolytic pathways, K-ATP channels, and 5' AMP-activated protein kinase (AMPK).[15] Common factors that influence adenine nucleotide levels, and therefore ADK activity are exercise, stress, changes in hormone levels, and diet.[15] It facilitates decoding of cellular information by catalyzing nucleotide exchange in the intimate “sensing zone” of metabolic sensors.[17]

ADK Shuttle

Adenylate kinase is present in mitochondrial and myofibrillar compartments in the cell, and it makes two high-energy phosphoryls (β and γ) of ATP available to be transferred between adenine nucleotide molecules.[15][16] In essence, adenylate kinase shuttles ATP to sites of high energy consumption and removes the AMP generated over the course of those reactions. These sequential phosphotransfer relays ultimately result in propagation of the phosphoryl groups along collections of ADK molecules.[15] This process can be thought of as a bucket brigade of ADK molecules that results in changes in local intracellular metabolic flux without apparent global changes in metabolite concentrations.[15] This process is extremely important for overall homeostasis of the cell.[15]

Disease relevance

Nucleoside diphosphate kinase deficiency

Nucleoside diphosphate (NDP) kinase catalyzes in vivo ATP-dependent synthesis of ribo- and deoxyribonucleoside triphosphates. In mutated Escherichia coli that had a disrupted nucleoside diphosphate kinase, adenylate kinase performed dual enzymatic functions. ADK complements nucleoside diphosphate kinase deficiency.[18]

Hemolytic anemia

Adenylate kinase deficiency in the erythrocyte is associated with hemolytic anemia.[19] This is a rare hereditary erythroenzymopathy that, in some cases, is associated with mental retardation and psychomotor impairment.[20] At least two patients have exhibited neonatal icterus and splenomegaly and required blood transfusions due to this deficiency.[21] In another patient, an abnormal fragment with homozygous and heterozygous A-->G substitutions at codon 164 caused severe erythrocyte ADK deficiency.[22] Two siblings had erythrocyte ADK deficiency, but one did not have evidence of hemolysis.[23]

AK1 and post-ischemic coronary reflow

Knock out of AK1 disrupts the synchrony between inorganic phosphate and turnover at ATP-consuming sites and ATP synthesis sites. This reduces the energetic signal communication in the post-ischemic heart and precipitates inadequate coronary reflow flowing ischemia-reperfusion.[24]

ADK2 deficiency

Adenylate Kinase 2 (AK2) deficiency in humans causes hematopoietic defects associated with sensorineural deafness.[25] Recticular dysgenesis is an autosomal recessive form of human combined immunodeficiency. It is also characterized by an impaired lymphoid maturation and early differentiation arrest in the myeloid lineage. AK2 deficiency results in absent or a large decrease in the expression of proteins. AK2 is specifically expressed in the stria vascularis of the inner ear which indicates why individuals with an AK2 deficiency will have sensorineural deafness.[25]

Structural adaptations

AK1 genetic ablation decreases tolerance to metabolic stress. AK1 deficiency induces fiber-type specific variation in groups of transcripts in glycolysis and mitochondrial metabolism.[26] This supports muscle energy metabolism.

Plastidial ADK deficiency in Arabidopsis thaliana

Enhanced growth and elevated photosynthetic amino acid is associated with plastidial adenylate kinase deficiency in Arabidopsis thaliana.[27]

References

  1. ^ The NIST Thermodynamics of Enzyme-Catalyzed Reactions database, http://xpdb.nist.gov/enzyme_thermodynamics/enzyme1.pl, Goldberg RN, Tewari YB, Bhat TN (November 2004). "Thermodynamics of enzyme-catalyzed reactions--a database for quantitative biochemistry". Bioinformatics. 20 (16): 2874–7. doi:10.1093/bioinformatics/bth314. PMID 15145806. , gives equilibrium constants, search for adenylate kinase under enzymes
  2. ^ Beis I, Newsholme EA (October 1975). "The contents of adenine nucleotides, phosphagens and some glycolytic intermediates in resting muscles from vertebrates and invertebrates". The Biochemical Journal. 152 (1): 23–32. doi:10.1042/bj1520023. PMC 1172435Freely accessible. PMID 1212224. 
  3. ^ a b Panayiotou C, Solaroli N, Karlsson A (April 2014). "The many isoforms of human adenylate kinases". The International Journal of Biochemistry & Cell Biology. 49: 75–83. doi:10.1016/j.biocel.2014.01.014. PMID 24495878. 
  4. ^ Panayiotou C, Solaroli N, Xu Y, Johansson M, Karlsson A (February 2011). "The characterization of human adenylate kinases 7 and 8 demonstrates differences in kinetic parameters and structural organization among the family of adenylate kinase isoenzymes". The Biochemical Journal. 433 (3): 527–34. doi:10.1042/BJ20101443. PMID 21080915. 
  5. ^ Tomasselli AG, Noda LH (January 1979). "Mitochondrial GTP-AMP phosphotransferase. 2. Kinetic and equilibrium dialysis studies". European Journal of Biochemistry. 93 (2): 263–7. doi:10.1111/j.1432-1033.1979.tb12819.x. PMID 218813. 
  6. ^ Cooper AJ, Friedberg EC (May 1992). "A putative second adenylate kinase-encoding gene from the yeast Saccharomyces cerevisiae". Gene. 114 (1): 145–8. doi:10.1016/0378-1119(92)90721-Z. PMID 1587477. 
  7. ^ a b Henzler-Wildman KA, Thai V, Lei M, Ott M, Wolf-Watz M, Fenn T, Pozharski E, Wilson MA, Petsko GA, Karplus M, Hübner CG, Kern D (December 2007). "Intrinsic motions along an enzymatic reaction trajectory". Nature. 450 (7171): 838–44. doi:10.1038/nature06410. PMID 18026086. 
  8. ^ Reinstein J, Gilles AM, Rose T, Wittinghofer A, Saint Girons I, Bârzu O, Surewicz WK, Mantsch HH (May 1989). "Structural and catalytic role of arginine 88 in Escherichia coli adenylate kinase as evidenced by chemical modification and site-directed mutagenesis". The Journal of Biological Chemistry. 264 (14): 8107–12. PMID 2542263. 
  9. ^ a b Müller CW, Schulz GE (March 1992). "Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state". Journal of Molecular Biology. 224 (1): 159–77. PMID 1548697. 
  10. ^ a b c Whitford PC, Miyashita O, Levy Y, Onuchic JN (March 2007). "Conformational transitions of adenylate kinase: switching by cracking". Journal of Molecular Biology. 366 (5): 1661–71. doi:10.1016/j.jmb.2006.11.085. PMC 2561047Freely accessible. PMID 17217965. 
  11. ^ Schrank TP, Bolen DW, Hilser VJ (October 2009). "Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins". Proceedings of the National Academy of Sciences of the United States of America. 106 (40): 16984–9. doi:10.1073/pnas.0906510106. PMC 2761315Freely accessible. PMID 19805185. 
  12. ^ Daily MD, Phillips GN, Cui Q (July 2010). "Many local motions cooperate to produce the adenylate kinase conformational transition". Journal of Molecular Biology. 400 (3): 618–31. doi:10.1016/j.jmb.2010.05.015. PMC 2902635Freely accessible. PMID 20471396. 
  13. ^ a b Rundqvist L, Adén J, Sparrman T, Wallgren M, Olsson U, Wolf-Watz M (March 2009). "Noncooperative folding of subdomains in adenylate kinase". Biochemistry. 48 (9): 1911–27. doi:10.1021/bi8018042. PMID 19219996. 
  14. ^ Olsson U, Wolf-Watz M (November 2010). "Overlap between folding and functional energy landscapes for adenylate kinase conformational change". Nature Communications. 1 (8): 111. doi:10.1038/ncomms1106. PMID 21081909. 
  15. ^ a b c d e f g Dzeja P, Terzic A (April 2009). "Adenylate kinase and AMP signaling networks: metabolic monitoring, signal communication and body energy sensing". International Journal of Molecular Sciences. 10 (4): 1729–72. doi:10.3390/ijms10041729. PMC 2680645Freely accessible. PMID 19468337. 
  16. ^ a b Dzeja PP, Chung S, Faustino RS, Behfar A, Terzic A (April 2011). "Developmental enhancement of adenylate kinase-AMPK metabolic signaling axis supports stem cell cardiac differentiation". PloS One. 6 (4): e19300. doi:10.1371/journal.pone.0019300. PMC 3083437Freely accessible. PMID 21556322. 
  17. ^ Dzeja P, Terzic A (April 2009). "Adenylate kinase and AMP signaling networks: metabolic monitoring, signal communication and body energy sensing". International Journal of Molecular Sciences. 10 (4): 1729–72. doi:10.3390/ijms10041729. PMC 2680645Freely accessible. PMID 19468337. 
  18. ^ Lu Q, Inouye M (June 1996). "Adenylate kinase complements nucleoside diphosphate kinase deficiency in nucleotide metabolism". Proceedings of the National Academy of Sciences of the United States of America. 93 (12): 5720–5. doi:10.1073/pnas.93.12.5720. PMC 39127Freely accessible. PMID 8650159. 
  19. ^ Matsuura, S.; Igarashi, M.; Tanizawa, Y.; Yamada, M.; Kishi, F.; Kajii, T.; Fujii, H.; Miwa, S.; Sakurai, M.; Nakazawa, A. (Jun 1989). "Human adenylate kinase deficiency associated with hemolytic anemia. A single base substitution affecting solubility and catalytic activity of the cytosolic adenylate kinase.". J Biol Chem. 264 (17): 10148–55. PMID 2542324. 
  20. ^ Abrusci P, Chiarelli LR, Galizzi A, Fermo E, Bianchi P, Zanella A, Valentini G (August 2007). "Erythrocyte adenylate kinase deficiency: characterization of recombinant mutant forms and relationship with nonspherocytic hemolytic anemia". Experimental Hematology. 35 (8): 1182–9. doi:10.1016/j.exphem.2007.05.004. PMID 17662886. 
  21. ^ Corrons JL, Garcia E, Tusell JJ, Varughese KI, West C, Beutler E (July 2003). "Red cell adenylate kinase deficiency: molecular study of 3 new mutations (118G>A, 190G>A, and GAC deletion) associated with hereditary nonspherocytic hemolytic anemia". Blood. 102 (1): 353–6. doi:10.1182/blood-2002-07-2288. PMID 12649162. 
  22. ^ Qualtieri, A.; Pedace, V.; Bisconte, MG.; Bria, M.; Gulino, B.; Andreoli, V.; Brancati, C. (Dec 1997). "Severe erythrocyte adenylate kinase deficiency due to homozygous A-->G substitution at codon 164 of human AK1 gene associated with chronic haemolytic anaemia.". Br J Haematol. 99 (4): 770–6. doi:10.1046/j.1365-2141.1997.4953299.x. PMID 9432020. 
  23. ^ Beutler E, Carson D, Dannawi H, Forman L, Kuhl W, West C, Westwood B (August 1983). "Metabolic compensation for profound erythrocyte adenylate kinase deficiency. A hereditary enzyme defect without hemolytic anemia". The Journal of Clinical Investigation. 72 (2): 648–55. doi:10.1172/JCI111014. PMC 1129224Freely accessible. PMID 6308059. 
  24. ^ Dzeja PP, Bast P, Pucar D, Wieringa B, Terzic A (October 2007). "Defective metabolic signaling in adenylate kinase AK1 gene knock-out hearts compromises post-ischemic coronary reflow". The Journal of Biological Chemistry. 282 (43): 31366–72. doi:10.1074/jbc.M705268200. PMC 3232003Freely accessible. PMID 17704060. 
  25. ^ a b Lagresle-Peyrou C, Six EM, Picard C, Rieux-Laucat F, Michel V, Ditadi A, Demerens-de Chappedelaine C, Morillon E, Valensi F, Simon-Stoos KL, Mullikin JC, Noroski LM, Besse C, Wulffraat NM, Ferster A, Abecasis MM, Calvo F, Petit C, Candotti F, Abel L, Fischer A, Cavazzana-Calvo M (January 2009). "Human adenylate kinase 2 deficiency causes a profound hematopoietic defect associated with sensorineural deafness". Nature Genetics. 41 (1): 106–11. doi:10.1038/ng.278. PMC 2612090Freely accessible. PMID 19043416. 
  26. ^ Janssen E, de Groof A, Wijers M, Fransen J, Dzeja PP, Terzic A, Wieringa B (April 2003). "Adenylate kinase 1 deficiency induces molecular and structural adaptations to support muscle energy metabolism". The Journal of Biological Chemistry. 278 (15): 12937–45. doi:10.1074/jbc.M211465200. PMID 12562761. 
  27. ^ Carrari F, Coll-Garcia D, Schauer N, Lytovchenko A, Palacios-Rojas N, Balbo I, Rosso M, Fernie AR (January 2005). "Deficiency of a plastidial adenylate kinase in Arabidopsis results in elevated photosynthetic amino acid biosynthesis and enhanced growth". Plant Physiology. 137 (1): 70–82. doi:10.1104/pp.104.056143. PMC 548839Freely accessible. PMID 15618410. 

External links

This article incorporates text from the public domain Pfam and InterPro IPR000850

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Adenylate kinase Provide feedback

No Pfam abstract.

Literature references

  1. Berry MB, Phillips GN Jr; , Proteins 1998;32:276-288.: Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+. PUBMED:9715904 EPMC:9715904


Internal database links

External database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Pfam Clan

This family is a member of clan P-loop_NTPase (CL0023), which has the following description:

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].

The clan contains the following 217 members:

6PF2K AAA AAA-ATPase_like AAA_10 AAA_11 AAA_12 AAA_13 AAA_14 AAA_15 AAA_16 AAA_17 AAA_18 AAA_19 AAA_2 AAA_21 AAA_22 AAA_23 AAA_24 AAA_25 AAA_26 AAA_27 AAA_28 AAA_29 AAA_3 AAA_30 AAA_31 AAA_32 AAA_33 AAA_34 AAA_35 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_Xtn Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arf ArgK ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 ATPase ATPase_2 Bac_DnaA BCA_ABC_TP_C Beta-Casp Cas_Csn2 Cas_St_Csn2 CbiA CBP_BcsQ CDC73_C CENP-M CFTR_R CLP1_P CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CSM2 CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DEAD DEAD_2 DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DUF1611 DUF1726 DUF2075 DUF2326 DUF2478 DUF257 DUF2791 DUF2813 DUF3584 DUF463 DUF815 DUF853 DUF87 DUF927 Dynamin_N Dynein_heavy ERCC3_RAD25_C Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GBP_C GTP_EFTU Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK Hydin_ADK IIGP IPPT IPT IstB_IS21 KAP_NTPase KdpD Kinesin KTI12 LAP1C Lon_2 LpxK MCM MEDS Mg_chelatase Microtub_bd MipZ MMR_HSR1 MMR_HSR1_C MobB MukB MutS_V Myosin_head NACHT NB-ARC NOG1 NTPase_1 NTPase_P4 ORC3_N ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK PSY3 Rad17 Rad51 Ras RecA ResIII RHD3 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2_N Spore_IV_A SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulphotransf T2SSE T4SS-DNA_transf Terminase_1 Terminase_3 Terminase_6 Terminase_GpA Thymidylate_kin TIP49 TK TniB Torsin TraG-D_C tRNA_lig_kinase TrwB_AAD_bind TsaE UvrB UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE Zeta_toxin Zot

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(21)
Full
(10091)
Representative proteomes UniProt
(23725)
NCBI
(30502)
Meta
(2542)
RP15
(2441)
RP35
(5570)
RP55
(8825)
RP75
(12310)
Jalview View  View  View  View  View  View  View  View  View 
HTML View                 
PP/heatmap 1                

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(21)
Full
(10091)
Representative proteomes UniProt
(23725)
NCBI
(30502)
Meta
(2542)
RP15
(2441)
RP35
(5570)
RP55
(8825)
RP75
(12310)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(21)
Full
(10091)
Representative proteomes UniProt
(23725)
NCBI
(30502)
Meta
(2542)
RP15
(2441)
RP35
(5570)
RP55
(8825)
RP75
(12310)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: adenylatekinase;
Type: Domain
Author: Finn RD
Number in seed: 21
Number in full: 10091
Average length of the domain: 166.80 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 61.40 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.8 26.8
Trusted cut-off 26.8 26.8
Noise cut-off 26.7 26.7
Model length: 151
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There are 3 interactions for this family. More...

ADK ADK_lid ADK_lid

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the ADK domain has been found. There are 161 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

Loading structure mapping...