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542  structures 8615  species 0  interactions 84450  sequences 581  architectures

Family: Epimerase (PF01370)

Summary: NAD dependent epimerase/dehydratase family

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 "NADH dehydrogenase (ubiquinone)". More...

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This is the Wikipedia entry entitled "UDP-glucose 4-epimerase". More...

UDP-glucose 4-epimerase Edit Wikipedia article

UDP-glucose 4-epimerase
Identifiers
AliasesUDPgalactose 4-epimerase4-epimeraseuridine diphosphate glucose 4-epimeraseUDPG-4-epimeraseUDP-galactose 4-epimeraseuridine diphosphoglucose epimeraseuridine diphospho-galactose-4-epimeraseUDP-D-galactose 4-epimeraseUDP-glucose epimeraseuridine diphosphoglucose 4-epimeraseuridine diphosphate galactose 4-epimerase
External IDsGeneCards: [1]
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

n/a

n/a

RefSeq (protein)

n/a

n/a

Location (UCSC)n/an/a
PubMed searchn/an/a
Wikidata
View/Edit Human
UDP-glucose 4-epimerase
Human GALE bound to NADH and UDP-glucose.png
H. sapiens UDP-glucose 4-epimerase homodimer bound to NADH and UDP-glucose. Domains: N-terminal and C-terminal.
Identifiers
EC no.5.1.3.2
CAS no.9032-89-7
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO
UDP-galactose-4-epimerase
Human GALE bound to NAD+ and UDP-GlcNAc.png
Human GALE bound to NAD+ and UDP-GlcNAc, with N- and C-terminal domains highlighted. Asn 207 contorts to accommodate UDP-GlcNAc within the active site.
Identifiers
SymbolGALE
NCBI gene2582
HGNC4116
OMIM606953
RefSeqNM_000403
UniProtQ14376
Other data
EC number5.1.3.2
LocusChr. 1 p36-p35
NAD-dependent epimerase/dehydratase
Identifiers
Symbol?
PfamPF01370
InterProIPR001509
Membranome330

The enzyme UDP-glucose 4-epimerase (EC 5.1.3.2), also known as UDP-galactose 4-epimerase or GALE, is a homodimeric epimerase found in bacterial, fungal, plant, and mammalian cells. This enzyme performs the final step in the Leloir pathway of galactose metabolism, catalyzing the reversible conversion of UDP-galactose to UDP-glucose.[1] GALE tightly binds nicotinamide adenine dinucleotide (NAD+), a co-factor required for catalytic activity.[2]

Additionally, human and some bacterial GALE isoforms reversibly catalyze the formation of UDP-N-acetylgalactosamine (UDP-GalNAc) from UDP-N-acetylglucosamine (UDP-GlcNAc) in the presence of NAD+, an initial step in glycoprotein or glycolipid synthesis.[3]

Historical significance

Dr. Luis Leloir deduced the role of GALE in galactose metabolism during his tenure at the Instituto de Investigaciones Bioquímicas del Fundación Campomar, initially terming the enzyme waldenase.[4] Dr. Leloir was awarded the 1970 Nobel Prize in Chemistry for his discovery of sugar nucleotides and their role in the biosynthesis of carbohydrates.[5]

Structure

GALE belongs to the short-chain dehydrogenase/reductase (SDR) superfamily of proteins.[6] This family is characterized by a conserved Tyr-X-X-X-Lys motif necessary for enzymatic activity; one or more Rossmann fold scaffolds; and the ability to bind NAD+.[6]

Tertiary structure

GALE structure has been resolved for a number of species, including E. coli[7] and humans.[8] GALE exists as a homodimer in various species.[8]

While subunit size varies from 68 amino acids (Enterococcus faecalis) to 564 amino acids (Rhodococcus jostii), a majority of GALE subunits cluster near 330 amino acids in length.[6] Each subunit contains two distinct domains. An N-terminal domain contains a 7-stranded parallel β-pleated sheet flanked by α-helices.[1] Paired Rossmann folds within this domain allow GALE to tightly bind one NAD+ cofactor per subunit.[2] A 6-stranded β-sheet and 5 α-helices comprise GALE's C-terminal domain.[1] C-terminal residues bind UDP, such that the subunit is responsible for correctly positioning UDP-glucose or UDP-galactose for catalysis.[1]

Active site

The cleft between GALE's N- and C-terminal domains constitutes the enzyme's active site. A conserved Tyr-X-X-X Lys motif is necessary for GALE catalytic activity; in humans, this motif is represented by Tyr 157-Gly-Lys-Ser-Lys 161,[6] while E. coli GALE contains Tyr 149-Gly-Lys-Ser-Lys 153.[8] The size and shape of GALE's active site varies across species, allowing for variable GALE substrate specificity.[3] Additionally, the conformation of the active site within a species-specific GALE is malleable; for instance, a bulky UDP-GlcNAc 2' N-acetyl group is accommodated within the human GALE active site by the rotation of the Asn 207 carboxamide side chain.[3]

Known E. coli GALE residue interactions with UDP-glucose and UDP-galactose.[9]
Residue Function
Ala 216, Phe 218 Anchor uracil ring to enzyme.
Asp 295 Interacts with ribose 2' hydroxyl group.
Asn 179, Arg 231, Arg 292 Interact with UDP phosphate groups.
Tyr 299, Asn 179 Interact with galactose 2' hydroxyl or glucose 6' hydroxyl group; properly position sugar within active site.
Tyr 177, Phe 178 Interact with galactose 3' hydroxyl or glucose 6' hydroxyl group; properly position sugar within active site.
Lys 153 Lowers pKa of Tyr 149, allows for abstraction or donation of a hydrogen atom to or from the sugar 4' hydroxyl group.
Tyr 149 Abstracts or donates a hydrogen atom to or from the sugar 4' hydroxyl group, catalyzing formation of 4-ketopyranose intermediate.

Mechanism

Conversion of UDP-galactose to UDP-glucose

GALE inverts the configuration of the 4' hydroxyl group of UDP-galactose through a series of 4 steps. Upon binding UDP-galactose, a conserved tyrosine residue in the active site abstracts a proton from the 4' hydroxyl group.[7][10]

Concomitantly, the 4' hydride is added to the si-face of NAD+, generating NADH and a 4-ketopyranose intermediate.[1] The 4-ketopyranose intermediate rotates 180° about the pyrophosphoryl linkage between the glycosyl oxygen and β-phosphorus atom, presenting the opposite face of the ketopyranose intermediate to NADH.[10] Hydride transfer from NADH to this opposite face inverts the stereochemistry of the 4' center. The conserved tyrosine residue then donates its proton, regenerating the 4' hydroxyl group.[1]

Conversion of UDP-GlcNAc to UDP-GalNAc

Human and some bacterial GALE isoforms reversibly catalyze the conversion of UDP-GlcNAc to UDP-GalNAc through an identical mechanism, inverting the stereochemical configuration at the sugar's 4' hydroxyl group.[3][11]

Biological function

Steps in the Leloir pathway of galactose metabolism.
Intermediates and enzymes in the Leloir pathway of galactose metabolism.[1]

Galactose metabolism

No direct catabolic pathways exist for galactose metabolism. Galactose is therefore preferentially converted into glucose-1-phosphate, which may be shunted into glycolysis or the inositol synthesis pathway.[12]

GALE functions as one of four enzymes in the Leloir pathway of galactose conversion of glucose-1-phosphate. First, galactose mutarotase converts β-D-galactose to α-D-galactose.[1] Galactokinase then phosphorylates α-D-galactose at the 1' hydroxyl group, yielding galactose-1-phosphate.[1] In the third step, galactose-1-phosphate uridyltransferase catalyzes the reversible transfer of a UMP moiety from UDP-glucose to galactose-1-phosphate, generating UDP-galactose and glucose-1-phosphate.[1] In the final Leloir step, UDP-glucose is regenerated from UDP-galactose by GALE; UDP-glucose cycles back to the third step of the pathway.[1] As such, GALE regenerates a substrate necessary for continued Leloir pathway cycling.

The glucose-1-phosphate generated in step 3 of the Leloir pathway may be isomerized to glucose-6-phosphate by phosphoglucomutase. Glucose-6-phosphate readily enters glycolysis, leading to the production of ATP and pyruvate.[13] Furthermore, glucose-6-phosphate may be converted to inositol-1-phosphate by inositol-3-phosphate synthase, generating a precursor needed for inositol biosynthesis.[14]

UDP-GalNAc synthesis

Human and selected bacterial GALE isoforms bind UDP-GlcNAc, reversibly catalyzing its conversion to UDP-GalNAc. A family of glycosyltransferases known as UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosamine transferases (ppGaNTases) transfers GalNAc from UDP-GalNAc to glycoprotein serine and threonine residues.[15] ppGaNTase-mediated glycosylation regulates protein sorting,[16][17][18][19][20] ligand signaling,[21][22][23] resistance to proteolytic attack,[24][25] and represents the first committed step in mucin biosynthesis.[15]

Role in disease

Human GALE deficiency or dysfunction results in Type III galactosemia, which may exist in a mild (peripheral) or more severe (generalized) form.[12]

References

  1. ^ a b c d e f g h i j k Holden HM, Rayment I, Thoden JB (November 2003). "Structure and function of enzymes of the Leloir pathway for galactose metabolism". J. Biol. Chem. 278 (45): 43885–8. doi:10.1074/jbc.R300025200. PMID 12923184.
  2. ^ a b Liu Y, Vanhooke JL, Frey PA (June 1996). "UDP-galactose 4-epimerase: NAD+ content and a charge-transfer band associated with the substrate-induced conformational transition". Biochemistry. 35 (23): 7615–20. doi:10.1021/bi960102v. PMID 8652544.
  3. ^ a b c d Thoden JB, Wohlers TM, Fridovich-Keil JL, Holden HM (May 2001). "Human UDP-galactose 4-epimerase. Accommodation of UDP-N-acetylglucosamine within the active site". J. Biol. Chem. 276 (18): 15131–6. doi:10.1074/jbc.M100220200. PMID 11279032.
  4. ^ LELOIR LF (September 1951). "The enzymatic transformation of uridine diphosphate glucose into a galactose derivative". Arch Biochem. 33 (2): 186–90. doi:10.1016/0003-9861(51)90096-3. hdl:11336/140700. PMID 14885999.
  5. ^ "The Nobel Prize in Chemistry 1970" (Press release). The Royal Swedish Academy of Science. 1970. Retrieved 2010-05-17.
  6. ^ a b c d Kavanagh KL, Jörnvall H, Persson B, Oppermann U (December 2008). "Medium- and short-chain dehydrogenase/reductase gene and protein families : the SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes". Cell. Mol. Life Sci. 65 (24): 3895–906. doi:10.1007/s00018-008-8588-y. PMC 2792337. PMID 19011750.
  7. ^ a b PDB: 1EK5​; Thoden JB, Wohlers TM, Fridovich-Keil JL, Holden HM (May 2000). "Crystallographic evidence for Tyr 157 functioning as the active site base in human UDP-galactose 4-epimerase". Biochemistry. 39 (19): 5691–701. doi:10.1021/bi000215l. PMID 10801319.
  8. ^ a b c PDB: 1XEL​; Thoden JB, Frey PA, Holden HM (April 1996). "Molecular structure of the NADH/UDP-glucose abortive complex of UDP-galactose 4-epimerase from Escherichia coli: implications for the catalytic mechanism". Biochemistry. 35 (16): 5137–44. doi:10.1021/bi9601114. PMID 8611497.
  9. ^ PDB: 1A9Z​; Thoden JB, Holden HM (August 1998). "Dramatic differences in the binding of UDP-galactose and UDP-glucose to UDP-galactose 4-epimerase from Escherichia coli". Biochemistry. 37 (33): 11469–77. doi:10.1021/bi9808969. PMID 9708982.
  10. ^ a b Liu Y, Thoden JB, Kim J, Berger E, Gulick AM, Ruzicka FJ, Holden HM, Frey PA (September 1997). "Mechanistic roles of tyrosine 149 and serine 124 in UDP-galactose 4-epimerase from Escherichia coli". Biochemistry. 36 (35): 10675–84. doi:10.1021/bi970430a. PMID 9271498.
  11. ^ Kingsley DM, Kozarsky KF, Hobbie L, Krieger M (March 1986). "Reversible defects in O-linked glycosylation and LDL receptor expression in a UDP-Gal/UDP-GalNAc 4-epimerase deficient mutant". Cell. 44 (5): 749–59. doi:10.1016/0092-8674(86)90841-X. PMID 3948246. S2CID 28293937.
  12. ^ a b Lai K, Elsas LJ, Wierenga KJ (November 2009). "Galactose toxicity in animals". IUBMB Life. 61 (11): 1063–74. doi:10.1002/iub.262. PMC 2788023. PMID 19859980.
  13. ^ Stryer, Lubert; Berg, Jeremy Mark; Tymoczko, John L. (2008). Biochemistry (Looseleaf). San Francisco: W. H. Freeman. pp. 443–58. ISBN 9780716718437.
  14. ^ Michell RH (February 2008). "Inositol derivatives: evolution and functions". Nat. Rev. Mol. Cell Biol. 9 (2): 151–61. doi:10.1038/nrm2334. PMID 18216771. S2CID 3245927.
  15. ^ a b Ten Hagen KG, Fritz TA, Tabak LA (January 2003). "All in the family: the UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases". Glycobiology. 13 (1): 1R–16R. doi:10.1093/glycob/cwg007. PMID 12634319.
  16. ^ Alfalah M, Jacob R, Preuss U, Zimmer KP, Naim H, Naim HY (June 1999). "O-linked glycans mediate apical sorting of human intestinal sucrase-isomaltase through association with lipid rafts". Curr. Biol. 9 (11): 593–6. doi:10.1016/S0960-9822(99)80263-2. PMID 10359703. S2CID 16866875.
  17. ^ Altschuler Y, Kinlough CL, Poland PA, Bruns JB, Apodaca G, Weisz OA, Hughey RP (March 2000). "Clathrin-mediated endocytosis of MUC1 is modulated by its glycosylation state". Mol. Biol. Cell. 11 (3): 819–31. doi:10.1091/mbc.11.3.819. PMC 14813. PMID 10712502.
  18. ^ Breuza L, Garcia M, Delgrossi MH, Le Bivic A (February 2002). "Role of the membrane-proximal O-glycosylation site in sorting of the human receptor for neurotrophins to the apical membrane of MDCK cells". Exp. Cell Res. 273 (2): 178–86. doi:10.1006/excr.2001.5442. PMID 11822873.
  19. ^ Naim HY, Joberty G, Alfalah M, Jacob R (June 1999). "Temporal association of the N- and O-linked glycosylation events and their implication in the polarized sorting of intestinal brush border sucrase-isomaltase, aminopeptidase N, and dipeptidyl peptidase IV". J. Biol. Chem. 274 (25): 17961–7. doi:10.1074/jbc.274.25.17961. PMID 10364244.
  20. ^ Zheng X, Sadler JE (March 2002). "Mucin-like domain of enteropeptidase directs apical targeting in Madin-Darby canine kidney cells". J. Biol. Chem. 277 (9): 6858–63. doi:10.1074/jbc.M109857200. PMID 11878264.
  21. ^ Hooper LV, Gordon JI (February 2001). "Glycans as legislators of host-microbial interactions: spanning the spectrum from symbiosis to pathogenicity". Glycobiology. 11 (2): 1R–10R. doi:10.1093/glycob/11.2.1R. PMID 11287395.
  22. ^ Yeh JC, Hiraoka N, Petryniak B, Nakayama J, Ellies LG, Rabuka D, Hindsgaul O, Marth JD, Lowe JB, Fukuda M (June 2001). "Novel sulfated lymphocyte homing receptors and their control by a Core1 extension beta 1,3-N-acetylglucosaminyltransferase". Cell. 105 (7): 957–69. doi:10.1016/S0092-8674(01)00394-4. PMID 11439191. S2CID 18674112.
  23. ^ Somers WS, Tang J, Shaw GD, Camphausen RT (October 2000). "Insights into the molecular basis of leukocyte tethering and rolling revealed by structures of P- and E-selectin bound to SLe(X) and PSGL-1". Cell. 103 (3): 467–79. doi:10.1016/S0092-8674(00)00138-0. PMID 11081633. S2CID 12719907.
  24. ^ Sauer J, Sigurskjold BW, Christensen U, Frandsen TP, Mirgorodskaya E, Harrison M, Roepstorff P, Svensson B (December 2000). "Glucoamylase: structure/function relationships, and protein engineering". Biochim. Biophys. Acta. 1543 (2): 275–293. doi:10.1016/s0167-4838(00)00232-6. PMID 11150611.
  25. ^ Garner B, Merry AH, Royle L, Harvey DJ, Rudd PM, Thillet J (June 2001). "Structural elucidation of the N- and O-glycans of human apolipoprotein(a): role of o-glycans in conferring protease resistance". J. Biol. Chem. 276 (25): 22200–8. doi:10.1074/jbc.M102150200. PMID 11294842.

Further reading

External links

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.

NAD dependent epimerase/dehydratase family Provide feedback

This family of proteins utilise NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions.

Literature references

  1. Thoden JB, Hegeman AD, Wesenberg G, Chapeau MC, Frey PA, Holden HM; , Biochemistry 1997;36:6294-6304.: Structural analysis of UDP-sugar binding to UDP-galactose 4-epimerase from Escherichia coli. PUBMED:9174344 EPMC:9174344


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001509

This domain is found in proteins that utilise NAD as a cofactor and use nucleotide-sugar substrates for a variety of chemical reactions [ PUBMED:9174344 ]. One of the best studied of these proteins is UDP-galactose 4-epimerase which catalyses the conversion of UDP-galactose to UDP-glucose during galactose metabolism [ PUBMED:11279032 , PUBMED:10801319 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

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Pfam Clan

This family is a member of clan NADP_Rossmann (CL0063), which has the following description:

A class of redox enzymes are two domain proteins. One domain, termed the catalytic domain, confers substrate specificity and the precise reaction of the enzyme. The other domain, which is common to this class of redox enzymes, is a Rossmann-fold domain. The Rossmann domain binds nicotinamide adenine dinucleotide (NAD+) and it is this cofactor that reversibly accepts a hydride ion, which is lost or gained by the substrate in the redox reaction. Rossmann domains have an alpha/beta fold, which has a central beta sheet, with approximately five alpha helices found surrounding the beta sheet.The strands forming the beta sheet are found in the following characteristic order 654123. The inter sheet crossover of the stands in the sheet form the NAD+ binding site [1]. In some more distantly relate Rossmann domains the NAD+ cofactor is replaced by the functionally similar cofactor FAD.

The clan contains the following 209 members:

2-Hacid_dh_C 3Beta_HSD 3HCDH_N 3HCDH_RFF adh_short adh_short_C2 ADH_zinc_N ADH_zinc_N_2 AdoHcyase_NAD AdoMet_MTase AlaDh_PNT_C Amino_oxidase ApbA AviRa B12-binding Bac_GDH Bin3 Bmt2 BMT5-like BpsA_C CARME CbiJ CheR CMAS CmcI CoA_binding CoA_binding_2 CoA_binding_3 Cons_hypoth95 CoV_ExoN CoV_Methyltr_2 DAO DapB_N DFP DNA_methylase DOT1 DRE2_N DREV DUF1442 DUF1611_N DUF166 DUF1776 DUF268 DUF2855 DUF3410 DUF364 DUF5129 DUF5130 DUF6094 DUF938 DXP_reductoisom DXPR_C Eco57I ELFV_dehydrog Eno-Rase_FAD_bd Eno-Rase_NADH_b Enoyl_reductase Epimerase F420_oxidored FAD_binding_2 FAD_binding_3 FAD_oxidored Fibrillarin FMO-like FmrO FtsJ fvmX7 G6PD_N GCD14 GDI GDP_Man_Dehyd GFO_IDH_MocA GIDA GidB GLF Glu_dehyd_C Glyco_hydro_4 Glyco_tran_WecG GMC_oxred_N Gp_dh_N GRAS GRDA HcgC HI0933_like HIM1 IlvN ISPD_C KR LCM Ldh_1_N LpxI_N Lycopene_cycl Lys_Orn_oxgnase Malic_M Mannitol_dh MCRA Met_10 Methyltr_RsmB-F Methyltr_RsmF_N Methyltrans_Mon Methyltrans_SAM Methyltransf_10 Methyltransf_11 Methyltransf_12 Methyltransf_14 Methyltransf_15 Methyltransf_16 Methyltransf_17 Methyltransf_18 Methyltransf_19 Methyltransf_2 Methyltransf_20 Methyltransf_21 Methyltransf_22 Methyltransf_23 Methyltransf_24 Methyltransf_25 Methyltransf_28 Methyltransf_29 Methyltransf_3 Methyltransf_30 Methyltransf_31 Methyltransf_32 Methyltransf_33 Methyltransf_34 Methyltransf_4 Methyltransf_5 Methyltransf_7 Methyltransf_8 Methyltransf_9 Methyltransf_PK MethyltransfD12 MetW Mg-por_mtran_C MmeI_Mtase MOLO1 Mqo MT-A70 MTS Mur_ligase N6-adenineMlase N6_Mtase N6_N4_Mtase NAD_binding_10 NAD_binding_2 NAD_binding_3 NAD_binding_4 NAD_binding_5 NAD_binding_7 NAD_binding_8 NAD_binding_9 NAD_Gly3P_dh_N NAS NmrA NNMT_PNMT_TEMT NodS OCD_Mu_crystall OpcA_G6PD_assem Orbi_VP4 PALP PARP_regulatory PCMT PDH_N PglD_N Polysacc_syn_2C Polysacc_synt_2 Pox_MCEL Pox_mRNA-cap Prenylcys_lyase PrmA PRMT5 Pyr_redox Pyr_redox_2 Pyr_redox_3 Reovirus_L2 RmlD_sub_bind Rossmann-like rRNA_methylase RrnaAD Rsm22 RsmJ Sacchrp_dh_NADP SAM_MT SE Semialdhyde_dh Shikimate_DH Spermine_synth SRR1 TehB THF_DHG_CYH_C Thi4 ThiF TPM_phosphatase TPMT TrkA_N TRM TRM13 TrmK tRNA_U5-meth_tr Trp_halogenase TylF Ubie_methyltran UDPG_MGDP_dh_N UPF0020 UPF0146 Urocanase V_cholerae_RfbT XdhC_C YjeF_N

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 and the UniProtKB sequence database. More...

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  Seed
(96)
Full
(84450)
Representative proteomes UniProt
(353592)
RP15
(10852)
RP35
(38724)
RP55
(82196)
RP75
(139646)
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  Seed
(96)
Full
(84450)
Representative proteomes UniProt
(353592)
RP15
(10852)
RP35
(38724)
RP55
(82196)
RP75
(139646)
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  Seed
(96)
Full
(84450)
Representative proteomes UniProt
(353592)
RP15
(10852)
RP35
(38724)
RP55
(82196)
RP75
(139646)
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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.

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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: Pfam-B_93 (release 3.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 96
Number in full: 84450
Average length of the domain: 220.70 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 65.97 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.9 20.9
Trusted cut-off 20.9 20.9
Noise cut-off 20.8 20.8
Model length: 241
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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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 Epimerase domain has been found. There are 542 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A096S670 View 3D Structure Click here
A0A0D1BUI1 View 3D Structure Click here
A0A0N7KPD6 View 3D Structure Click here
A0A0N7KQ50 View 3D Structure Click here
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