Summary: Cobalamin adenosyltransferase

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Wikipedia: Cob(I)yrinic acid a,c-diamide adenosyltransferase
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This is the Wikipedia entry entitled "Cob(I)yrinic acid a,c-diamide adenosyltransferase". More...

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

ATP:corrinoid adenosyltransferase

the three-dimensional structure of atp:corrinoid adenosyltransferase from salmonella typhimurium. apo-atp form

Identifiers

Symbol

CobA_CobO_BtuR

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Cobalamin adenosyltransferase (PduO/EutT)

crystal structure of conserved protein 0546 from thermoplasma acidophilum

Identifiers

Symbol

Cob_adeno_trans

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

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]

[edit] References

^ ^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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC524904/.
^ ^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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1482872/.
^ 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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC516830/.
^ 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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC95042/.
^ 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.
^ 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.
^ 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.

Cobalamin adenosyltransferase Provide feedback

Cobalamin adenosyltransferase This family contains the gene products of PduO and EutT which are both cobalamin adenosyltransferases. PduO is a protein with ATP:cob(I)alamin adenosyltransferase activity. The main role of this protein is the conversion of inactive cobalamins to AdoCbl for 1,2-propanediol degradation [1].The EutT enzyme appears to be an adenosyl transferase, converting CNB12 to AdoB12 [2].

Literature references

Johnson CL, Pechonick E, Park SD, Havemann GD, Leal NA, Bobik TA; , J Bacteriol 2001;183:1577-1584.: Functional genomic, biochemical, and genetic characterization of the Salmonella pduO gene, an ATP:cob(I)alamin adenosyltransferase gene. PUBMED:11160088 EPMC:11160088
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

External database links

PANDIT:	PF01923
Pseudofam:	PF01923
SCOP:	1nog
SYSTERS:	Cob_adeno_trans

This tab holds annotation information from the InterPro database.

InterPro entry IPR002779

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 EutT- and PduO-type ATP:cob(I)alamin adenosyltransferases. PduO functions to convert cobalamin to AdoCbl for 1,2-propanediol degradation [PUBMED:9311132], while EutT produces AdoCbl for ethanolamine utilisation [PUBMED:16636051].

Gene Ontology

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

Molecular function	ATP binding (GO:0005524)
Molecular function	cob(I)yrinic acid a,c-diamide adenosyltransferase activity (GO:0008817)
Biological process	cobalamin biosynthetic process (GO:0009236)

Domain organisation

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

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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...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

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PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
Pfam viewer: an HTML-based viewer that uses DAS to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

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Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

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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 (180)	Full (2946)	Representative proteomes				NCBI (2068)	Meta (1103)
	Seed (180)	Full (2946)	RP15 (266)	RP35 (472)	RP55 (598)	RP75 (715)	NCBI (2068)	Meta (1103)
Jalview	View	View	View	View	View	View	View	View
HTML	View	View	View	View	View	View
PP/heatmap	₁	View	View	View	View	View
Pfam viewer	View	View

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

Key: available, not generated, — not available.

Format an alignment

	Seed (180)	Full (2946)	Representative proteomes				NCBI (2068)	Meta (1103)
	Seed (180)	Full (2946)	RP15 (266)	RP35 (472)	RP55 (598)	RP75 (715)	NCBI (2068)	Meta (1103)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	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 (180)	Full (2946)	Representative proteomes				NCBI (2068)	Meta (1103)
	Seed (180)	Full (2946)	RP15 (266)	RP35 (472)	RP55 (598)	RP75 (715)	NCBI (2068)	Meta (1103)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	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.

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.

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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

Seed source:

Enright A

Previous IDs:

DUF80;

Type:

Domain

Author:

Moxon SJ

Number in seed:

180

Number in full:

2946

Average length of the domain:

162.40 aa

Average identity of full alignment:

34 %

Average coverage of the sequence by the domain:

75.35 %

HMM information

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	21.3	21.3
Trusted cut-off	21.3	21.4
Noise cut-off	21.1	21.1

Model length:

163

Family (HMM) version:

13

Download:

download the raw HMM for this family

Species distribution

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How the sunburst is generated

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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

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Interactive tree

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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We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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Interactions

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

Cob_adeno_trans

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 Cob_adeno_trans domain has been found. There are 41 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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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Cob_adeno_trans (PF01923)

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Summary: Cobalamin adenosyltransferase

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

[edit] References

Cobalamin adenosyltransferase Provide feedback

Literature references

External database links

InterPro entry IPR002779

Gene Ontology

Domain organisation

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

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Colour assignments

Selections

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How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

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Selected sequences

Species trees

Interactive tree

Interactions

Structures