Summary: Ethanolamine utilisation protein EutN/carboxysome
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Ethanolamine utilisation protein EutN/carboxysome Provide feedback
The crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel ( PDB:2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a hole in the center. this suggests that EutN forms a pore, with an opening of 26 Angstrom in diameter on one face and 14 Angstrom on the other face . EutN is involved in the cobalamin-dependent degradation of ethanolamine .
Kofoid E, Rappleye C, Stojiljkovic I, Roth J; , J Bacteriol 1999;181:5317-5329.: The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. PUBMED:10464203 EPMC:10464203
Forouhar F, Kuzin A, Seetharaman J, Lee I, Zhou W, Abashidze M, Chen Y, Yong W, Janjua H, Fang Y, Wang D, Cunningham K, Xiao R, Acton TB, Pichersky E, Klessig DF, Porter CW, Montelione GT, Tong L;, J Struct Funct Genomics. 2007;8:37-44.: Functional insights from structural genomics. PUBMED:17588214 EPMC:17588214
This tab holds annotation information from the InterPro database.
InterPro entry IPR004992
This entry represents a family of related bacterial proteins with roles in ethanolamine and carbon dioxide metabolism.
The ethanolamine utilization protein EutN is involved in the cobalamin-dependent degradation of ethanolamine [ PUBMED:10464203 ]. The crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (PDB: 2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a hole in the centre. This suggests that EutN forms a pore, with an opening of 26 Amstrong in diameter on one face and 14 Amstrong on the other face [ PUBMED:17588214 ].
Beside the Escherichia coli ethanolamine utilization protein EutN and the Synechocystis sp. carboxysome (beta-type) structural protein CcmL, this family also includes alpha-type carboxysome structural proteins CsoS4A and CsoS4B (previously known as OrfA and OrfB), propanediol utilization protein PduN, and some hypothetical homologous of various bacterial microcompartments. The carboxysome, a polyhedral organelle, participates in carbon fixation by sequestering enzymes. It is the prototypical bacterial microcompartment. Its enzymatic components, ribulose bisphosphate carboxylase/oxygenase(RuBisCO) and carbonic anhydrase (CA), are surrounded by a polyhedral protein shell. Similarly, the ethanolamine utilization (eut) microcompartment, and the 1,2-propanediol utilization (pdu) microcompartment encapsulate the enzymes necessary for the process of cobalamin-dependent ethanolamine degradation, and coenzyme B12-dependent degradation of 1,2-propanediol, respectively, within its polyhedral protein shells. It is interesting that both carboxysome structural proteins CcmL and CsoS4A assemble as pentamers in the crystal structures, which might constitute the twelve pentameric vertices of a regular icosahedral carboxysome. However, the reported EutN structure is hexameric rather than pentameric. The absence of pentamers in Eut microcompartments might lead to less-regular icosahedral shell shapes. Due to the lack of structure evidence, the functional roles of the CsoS4A adjacent paralog, CsoS4B, and propanediol utilization protein PduN are not yet clear [ PUBMED:10464203 , PUBMED:19177356 , PUBMED:18248510 , PUBMED:17511640 , PUBMED:18258595 , PUBMED:18937343 , PUBMED:17578868 , PUBMED:19172747 , PUBMED:16525780 , PUBMED:18679172 , PUBMED:15862091 , PUBMED:12554704 , PUBMED:11722879 , PUBMED:18974784 , PUBMED:17897412 , PUBMED:18332146 , PUBMED:18292340 , PUBMED:17993516 , PUBMED:2656649 , PUBMED:17669419 , PUBMED:3045078 , PUBMED:4127632 , PUBMED:4355679 , PUBMED:7868611 , PUBMED:7934888 , PUBMED:8491708 , PUBMED:9245772 , PUBMED:9891798 , PUBMED:12520366 , PUBMED:12923081 , PUBMED:14729686 , PUBMED:15516577 , PUBMED:16081736 , PUBMED:16385071 , PUBMED:16585748 , PUBMED:17028023 , PUBMED:179979 , PUBMED:190964 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||polyhedral organelle (GO:0031469)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin . The common part of the OB-fold, has a five-stranded beta-sheet coiled to form a closed beta-barrel. This barrel is capped by an alpha-helix located between the third and fourth strands .
The clan contains the following 113 members:BOF BRCA-2_OB1 BRCA-2_OB3 CcmE CDC13_N Cdc13_OB2 CDC24_OB1 CDC24_OB2 CDC24_OB3 CSD CSD2 CusF_Ec CysA_C_terminal DNA_ligase_A_C DNA_ligase_C DNA_ligase_OB DNA_ligase_OB_2 DNA_pol_D_N DUF1344 DUF1449 DUF2110 DUF223 DUF2815 DUF3127 DUF3217 DUF3299 DUF5666 DUF6484 DUF961 EFP eIF-1a eIF-5a Elong-fact-P_C EutN_CcmL EXOSC1 FbpC_C_terminal Fimbrial_PilY2 GlcV_C_terminal Gp138_N gp32 Gp5_OB HIN HROB ID MCM_OB mRNA_cap_C MRP-S35 NfeD NigD_N NlpE_C OB_aCoA_assoc OB_Dis3 OB_MalK OB_NTP_bind OB_RNB PCB_OB Phage_base_V Phage_DNA_bind Phage_SSB Pol_alpha_B_N POT1 POT1PC Prot_ATP_ID_OB Prot_ATP_OB_N RecG_wedge RecJ_OB RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 Rep_fac-A_C REPA_OB_2 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 Ribosomal_S28e Ribosomal_S4e RMI1_C RMI1_N RMI2 RNA_pol_Rbc25 RNA_pol_Rpb8 RNA_pol_RpbG RNase_II_C_S1 RPA43_OB Rrp44_CSD1 Rrp44_S1 RsgA_N RuvA_N S1 S1-like S1_2 SfsA_N SSB ssDBP Stn1 TEBP_beta Ten1 Ten1_2 TLP1_add_C TOBE TOBE_2 TOBE_3 TPP1 TRAM TRAM_2 tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind TTC5_OB WCOB
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Seed source:||Pfam-B_3053 (release 6.5)|
|Number in seed:||174|
|Number in full:||1571|
|Average length of the domain:||82.40 aa|
|Average identity of full alignment:||38 %|
|Average coverage of the sequence by the domain:||89.30 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
|Download:||download the raw HMM for this family|
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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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 EutN_CcmL domain has been found. There are 420 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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