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10  structures 1439  species 2  interactions 1655  sequences 18  architectures

Family: FTCD_C (PF04961)

Summary: Formiminotransferase-cyclodeaminase

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This is the Wikipedia entry entitled "Cyclodeaminase domain". More...

Cyclodeaminase domain Edit Wikipedia article

FTCD_C
PDB 1o5h EBI.jpg
crystal structure of formiminotetrahydrofolate cyclodeaminase (tm1560) from thermotoga maritima at 2.80 a resolution
Identifiers
Symbol FTCD_C
Pfam PF04961
InterPro IPR007044
SCOP 1o5h
SUPERFAMILY 1o5h

In molecular biology, enzymes containing the cyclodeaminase domain function in channeling one-carbon units to the folate pool. In most cases, this domain acts as a formimidoyltetrahydrofolate cyclodeaminase, which catalyses the cyclisation of formimidoyltetrahydrofolate to methenyltetrahydrofolate as shown in reaction (1). In the methylotrophic bacterium Methylobacterium extorquens, however, it acts as a methenyltetrahydrofolate cyclohydrolase, which catalyses the interconversion of formyltetrahydrofolate and methylenetetrahydrofolate, as shown in reaction (2).[1]

(1) 5-formimidoyltetrahydrofolate = 5,10-methenyltetrahydrofolate + NH(3)

(2) 10- formyltetrahydrofolate = 5,10-methenyltetrahydrofolate + H(2)O

In prokaryotes, this domain mostly occurs on its own, while in eukaryotes it is fused to a glutamate formiminotransferase domain (which catalyses the previous step in the pathway) to form the bifunctional enzyme formiminotransferase cyclodeaminase.[2] The eukaryotic enzyme is a circular tetramer of homodimers, while the prokaryotic enzyme is a dimer.[1][3][4]

The crystal structure of the cyclodeaminase enzyme from Thermaotogoa maritima has been studied.[4] It is a homodimer, where each monomer is composed of six alpha helices arranged in an up and down helical bundle, forming a novel fold. The location of the active site is not known, but sequence alignments revealed two clusters of conserved residues located in a deep pocket within the dimmer interface. This pocket was large enough to accommodate the reaction product and it was postulated that this is the active site.

References

  1. ^ a b Pomper BK, Vorholt JA, Chistoserdova L, Lidstrom ME, Thauer RK (April 1999). "A methenyl tetrahydromethanopterin cyclohydrolase and a methenyl tetrahydrofolate cyclohydrolase in Methylobacterium extorquens AM1". Eur. J. Biochem. 261 (2): 475–80. doi:10.1046/j.1432-1327.1999.00291.x. PMID 10215859. 
  2. ^ Murley LL, MacKenzie RE (August 1995). "The two monofunctional domains of octameric formiminotransferase-cyclodeaminase exist as dimers". Biochemistry. 34 (33): 10358–64. doi:10.1021/bi00033a006. PMID 7654689. 
  3. ^ MacKenzie RE, Aldridge M, Paquin J (October 1980). "The bifunctional enzyme formiminotransferase-cyclodeaminase is a tetramer of dimers". J. Biol. Chem. 255 (19): 9474–8. PMID 7410436. 
  4. ^ a b Xu Q, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Biorac T, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hampton E, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Reyes R, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, White A, Wolf G, Zagnitko O, Hodgson KO, Wooley J, Wilson IA (March 2005). "Crystal structure of a formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution reveals a new fold". Proteins. 58 (4): 976–81. doi:10.1002/prot.20364. PMID 15651027. 

This article incorporates text from the public domain Pfam and InterPro IPR007044

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

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Formiminotransferase-cyclodeaminase Provide feedback

Members of this family are thought to be Formiminotransferase- cyclodeaminase enzymes EC:4.3.1.4. This domain is found in the C-terminus of the bifunctional animal members of the family.

Literature references

  1. Murley LL, MacKenzie RE; , Biochemistry 1995;34:10358-10364.: The two monofunctional domains of octameric formiminotransferase-cyclodeaminase exist as dimers. PUBMED:7654689 EPMC:7654689


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007044

Enzymes containing the cyclodeaminase domain function in channelling one-carbon units to the folate pool. In most cases, this domain catalyses the cyclisation of formimidoyltetrahydrofolate to methenyltetrahydrofolate as shown in reaction (1). In the methylotrophic bacterium Methylobacterium extorquens, however, it catalyses the interconversion of formyltetrahydrofolate and methylenetetrahydrofolate [PUBMED:10215859],as shown in reaction (2)

(1) 5-formimidoyltetrahydrofolate = 5,10-methenyltetrahydrofolate + NH(3)

(2) 10- formyltetrahydrofolate = 5,10-methenyltetrahydrofolate + H(2)O

In prokaryotes, this domain mostly occurs on its own, while in eukaryotes it is fused to a glutamate formiminotransferase domain (which catalyses the previous step in the pathway) to form the bifunctional enzyme formiminotransferase-cyclodeaminase [PUBMED:7654689]. The eukaryotic enzyme is a circular tetramer of homodimers [PUBMED:7410436], while the prokaryotic enzyme is a dimer [PUBMED:10215859, PUBMED:15651027].

The crystal structure of the cyclodeaminase enzyme (SWISSPROT) from Thermaotoga maritima has been studied [PUBMED:15651027]. It is a homodimer, where each monomer is composed of six alpha helices arranged in an up and down helical bundle, forming a novel fold. The location of the active site is not known, but sequence alignments revealed two clusters of conserved residues located in a deep pocket within the dimmer interface. This pocket was large enough to accommodate the reaction product and it was postulated that this is the active site.

Gene Ontology

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Domain organisation

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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 (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...

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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
(284)
Full
(1655)
Representative proteomes UniProt
(4510)
NCBI
(5153)
Meta
(206)
RP15
(600)
RP35
(1303)
RP55
(1707)
RP75
(2244)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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  Seed
(284)
Full
(1655)
Representative proteomes UniProt
(4510)
NCBI
(5153)
Meta
(206)
RP15
(600)
RP35
(1303)
RP55
(1707)
RP75
(2244)
Alignment:
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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
(284)
Full
(1655)
Representative proteomes UniProt
(4510)
NCBI
(5153)
Meta
(206)
RP15
(600)
RP35
(1303)
RP55
(1707)
RP75
(2244)
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

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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

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Curation View help on the curation process

Seed source: COG3404
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 284
Number in full: 1655
Average length of the domain: 175.50 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 61.93 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.5 23.5
Trusted cut-off 23.5 24.5
Noise cut-off 22.9 23.3
Model length: 182
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

FTCD FTCD_C

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 FTCD_C domain has been found. There are 10 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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