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4  structures 2106  species 1  interaction 2528  sequences 9  architectures

Family: CobA_CobO_BtuR (PF02572)

Summary: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

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 "Cob(I)yrinic acid a,c-diamide adenosyltransferase". More...

Cob(I)yrinic acid a,c-diamide adenosyltransferase Edit Wikipedia article

ATP:corrinoid adenosyltransferase
PDB 1g5t EBI.jpg
the three-dimensional structure of atp:corrinoid adenosyltransferase from salmonella typhimurium. apo-atp form
Identifiers
Symbol CobA_CobO_BtuR
Pfam PF02572
Pfam clan CL0023
InterPro IPR003724
SCOP 1g64
SUPERFAMILY 1g64
Cobalamin adenosyltransferase (PduO/EutT)
PDB 1nog EBI.jpg
crystal structure of conserved protein 0546 from thermoplasma acidophilum
Identifiers
Symbol Cob_adeno_trans
Pfam PF01923
InterPro IPR002779
SCOP 1nog
SUPERFAMILY 1nog

In molecular biology, cob(I)yrinic acid a,c-diamide adenosyltransferase (also known as ATP:cob(I)alamin or ATP:corrinoid adenosyltransferase) EC 2.5.1.17 is an enzyme which catalyses the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12).[1] Adenosylcobalamin (AdoCbl) is required for the activity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type,[2] EutT-type [3] and PduO-type.[4] Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis of AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution.

The CobA group includes the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins.[5] CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the conversion of cobalamin to adenosylcobalamin.[1][2] PduO functions to convert cobalamin to AdoCbl for 1,2-propanediol degradation,[6] while EutT produces AdoCbl for ethanolamine utilisation.[7]

References[edit]

  1. ^ a b Sheppard DE, Penrod JT, Bobik T, Kofoid E, Roth JR (November 2004). "Evidence that a B12-adenosyl transferase is encoded within the ethanolamine operon of Salmonella enterica". J. Bacteriol. 186 (22): 7635–44. doi:10.1128/JB.186.22.7635-7644.2004. PMC 524904. PMID 15516577. 
  2. ^ a b Buan NR, Rehfeld K, Escalante-Semerena JC (May 2006). "Studies of the CobA-type ATP:Co(I)rrinoid adenosyltransferase enzyme of Methanosarcina mazei strain Go1". J. Bacteriol. 188 (10): 3543–50. doi:10.1128/JB.188.10.3543-3550.2006. PMC 1482872. PMID 16672609. 
  3. ^ Buan NR, Suh SJ, Escalante-Semerena JC (September 2004). "The eutT gene of Salmonella enterica Encodes an oxygen-labile, metal-containing ATP:corrinoid adenosyltransferase enzyme". J. Bacteriol. 186 (17): 5708–14. doi:10.1128/JB.186.17.5708-5714.2004. PMC 516830. PMID 15317775. 
  4. ^ Johnson CL, Pechonick E, Park SD, Havemann GD, Leal NA, Bobik TA (March 2001). "Functional genomic, biochemical, and genetic characterization of the Salmonella pduO gene, an ATP:cob(I)alamin adenosyltransferase gene". J. Bacteriol. 183 (5): 1577–84. doi:10.1128/JB.183.5.1577-1584.2001. PMC 95042. PMID 11160088. 
  5. ^ Suh SJ, Escalante-Semerena JC (July 1993). "Cloning, sequencing and overexpression of cobA which encodes ATP:corrinoid adenosyltransferase in Salmonella typhimurium". Gene 129 (1): 93–7. doi:10.1016/0378-1119(93)90701-4. PMID 7916712. 
  6. ^ Luers F, Seyfried M, Daniel R, Gottschalk G (September 1997). "Glycerol conversion to 1,3-propanediol by Clostridium pasteurianum: cloning and expression of the gene encoding 1,3-propanediol dehydrogenase". FEMS Microbiol. Lett. 154 (2): 337–45. PMID 9311132. 
  7. ^ Buan NR, Escalante-Semerena JC (June 2006). "Purification and initial biochemical characterization of ATP:Cob(I)alamin adenosyltransferase (EutT) enzyme of Salmonella enterica". J. Biol. Chem. 281 (25): 16971–7. doi:10.1074/jbc.M603069200. PMID 16636051. 

This article incorporates text from the public domain Pfam and InterPro IPR003724

This article incorporates text from the public domain Pfam and InterPro IPR002779

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.

ATP:corrinoid adenosyltransferase BtuR/CobO/CobP Provide feedback

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin adenosyltransferase, EC:2.5.1.17, involved in cobalamin (vitamin B12) biosynthesis. These enzymes catalyse the adenosylation reaction: ATP + cob(I)alamin + H2O <=> phosphate + diphosphate + adenosylcobalamin.

Literature references

  1. Raux E, Lanois A, Warren MJ, Rambach A, Thermes C; , Biochem J 1998;335:159-166.: Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon. PUBMED:9742225 EPMC:9742225


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003724

ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) [PUBMED:15516577]. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [PUBMED:16672609], EutT-type [PUBMED:15317775] and PduO-type [PUBMED:11160088]. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution.

This entry represents the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins [PUBMED:7916712]. CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin [PUBMED:16672609, PUBMED:15516577].

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 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 198 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_4 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_2 Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arch_ATPase Arf ArgK ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 Bac_DnaA CbiA CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT 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 DUF1253 DUF1611 DUF2075 DUF2478 DUF258 DUF2791 DUF2813 DUF3584 DUF463 DUF815 DUF853 DUF87 DUF927 Dynamin_N Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GTP_EFTU GTP_EFTU_D2 GTP_EFTU_D4 Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK IIGP IPPT IPT IstB_IS21 KaiC KAP_NTPase Kinesin Kinesin-relat_1 Kinesin-related KTI12 LpxK MCM MEDS Mg_chelatase Mg_chelatase_2 MipZ Miro MMR_HSR1 MobB MukB MutS_V Myosin_head NACHT NB-ARC NOG1 NTPase_1 ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK Rad17 Rad51 Ras RecA ResIII RHD3 RHSP RNA12 RNA_helicase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2_N Spore_IV_A SRP54 SRPRB Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulphotransf T2SE 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 UPF0079 UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE YhjQ 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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(173)
Full
(2528)
Representative proteomes NCBI
(1797)
Meta
(875)
RP15
(192)
RP35
(403)
RP55
(529)
RP75
(629)
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  Seed
(173)
Full
(2528)
Representative proteomes NCBI
(1797)
Meta
(875)
RP15
(192)
RP35
(403)
RP55
(529)
RP75
(629)
Alignment:
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  Seed
(173)
Full
(2528)
Representative proteomes NCBI
(1797)
Meta
(875)
RP15
(192)
RP35
(403)
RP55
(529)
RP75
(629)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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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: COGs
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A
Number in seed: 173
Number in full: 2528
Average length of the domain: 170.90 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 88.83 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.4 23.4
Trusted cut-off 23.7 26.2
Noise cut-off 23.2 22.9
Model length: 172
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

CobA_CobO_BtuR

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 CobA_CobO_BtuR domain has been found. There are 4 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.

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