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296  structures 4814  species 3  interactions 10559  sequences 39  architectures

Family: OTCace (PF00185)

Summary: Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain

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This is the Wikipedia entry entitled "ATCase/OTCase family". More...

ATCase/OTCase family Edit Wikipedia article

Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
PDB 1ml4 EBI.jpg
the pala-liganded aspartate transcarbamoylase catalytic subunit from pyrococcus abyssi
Identifiers
Symbol OTCace_N
Pfam PF02729
InterPro IPR006132
PROSITE PDOC00091
SCOP 1raa
SUPERFAMILY 1raa
Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
Identifiers
Symbol OTCace
Pfam PF00185
SCOP 1raa
SUPERFAMILY 1raa

In molecular biology, the ATCase/OTCase family is a protein family which contains two related enzymes: aspartate carbamoyltransferase EC 2.1.3.2 and ornithine carbamoyltransferase EC 2.1.3.3. It has been shown that these enzymes are evolutionary related.[1] The predicted secondary structure of both enzymes is similar and there are some regions of sequence similarities. One of these regions includes three residues which have been shown, by crystallographic studies to be implicated in binding the phosphoryl group of carbamoyl phosphate and may also play a role in trimerisation of the molecules.[2][3] The N-terminal domain is the carbamoyl phosphate binding domain. The C-terminal domain is an aspartate/ornithine-binding domain.

Aspartate carbamoyltransferase (ATCase) catalyses the conversion of aspartate and carbamoyl phosphate to carbamoylaspartate, the second step in the de novo biosynthesis of pyrimidine nucleotides.[4] In prokaryotes ATCase consists of two subunits: a catalytic chain (gene pyrB) and a regulatory chain (gene pyrI), while in eukaryotes it is a domain in a multi- functional enzyme (called URA2 in yeast, rudimentary in Drosophila, and CAD in mammals) that also catalyzes other steps of the biosynthesis of pyrimidines.[5]

Ornithine carbamoyltransferase (OTCase) catalyses the conversion of ornithine and carbamoyl phosphate to citrulline. In mammals this enzyme participates in the urea cycle and is located in the mitochondrial matrix.[6] In prokaryotes and eukaryotic microorganisms it is involved in the biosynthesis of arginine. In some bacterial species it is also involved in the degradation of arginine (the arginine deaminase pathway).[7]

References[edit]

  1. ^ Houghton JE, Bencini DA, O'Donovan GA, Wild JR (August 1984). "Protein differentiation: a comparison of aspartate transcarbamoylase and ornithine transcarbamoylase from Escherichia coli K-12". Proc. Natl. Acad. Sci. U.S.A. 81 (15): 4864–8. doi:10.1073/pnas.81.15.4864. PMC 391592. PMID 6379651. 
  2. ^ Ke HM, Honzatko RB, Lipscomb WN (July 1984). "Structure of unligated aspartate carbamoyltransferase of Escherichia coli at 2.6-A resolution". Proc. Natl. Acad. Sci. U.S.A. 81 (13): 4037–40. doi:10.1073/pnas.81.13.4037. PMC 345363. PMID 6377306. 
  3. ^ Beernink PT, Endrizzi JA, Alber T, Schachman HK (May 1999). "Assessment of the allosteric mechanism of aspartate transcarbamoylase based on the crystalline structure of the unregulated catalytic subunit". Proc. Natl. Acad. Sci. U.S.A. 96 (10): 5388–93. doi:10.1073/pnas.96.10.5388. PMC 21869. PMID 10318893. 
  4. ^ Lerner CG, Switzer RL (August 1986). "Cloning and structure of the Bacillus subtilis aspartate transcarbamylase gene (pyrB)". J. Biol. Chem. 261 (24): 11156–65. PMID 3015959. 
  5. ^ Davidson JN, Chen KC, Jamison RS, Musmanno LA, Kern CB (March 1993). "The evolutionary history of the first three enzymes in pyrimidine biosynthesis". BioEssays 15 (3): 157–64. doi:10.1002/bies.950150303. PMID 8098212. 
  6. ^ Takiguchi M, Matsubasa T, Amaya Y, Mori M (May 1989). "Evolutionary aspects of urea cycle enzyme genes". BioEssays 10 (5): 163–6. doi:10.1002/bies.950100506. PMID 2662961. 
  7. ^ Baur H, Stalon V, Falmagne P, Luethi E, Haas D (July 1987). "Primary and quaternary structure of the catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa. Extensive sequence homology with the anabolic ornithine carbamoyltransferases of Escherichia coli". Eur. J. Biochem. 166 (1): 111–7. doi:10.1111/j.1432-1033.1987.tb13489.x. PMID 3109911. 

This article incorporates text from the public domain Pfam and InterPro IPR006132

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Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain Provide feedback

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Literature references

  1. Beernink PT, Endrizzi JA, Alber T, Schachman HK; , Proc Natl Acad Sci U S A 1999;96:5388-5393.: Assessment of the allosteric mechanism of aspartate transcarbamoylase based on the crystalline structure of the unregulated catalytic subunit. PUBMED:10318893 EPMC:10318893


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006131

This family contains two related enzymes:

  1. Aspartate carbamoyltransferase (EC) (ATCase) catalyzes the conversion of aspartate and carbamoyl phosphate to carbamoylaspartate, the second step in the de novo biosynthesis of pyrimidine nucleotides [PUBMED:3015959]. In prokaryotes ATCase consists of two subunits: a catalytic chain (gene pyrB) and a regulatory chain (gene pyrI), while in eukaryotes it is a domain in a multi- functional enzyme (called URA2 in yeast, rudimentary in Drosophila, and CAD in mammals [PUBMED:8098212]) that also catalyzes other steps of the biosynthesis of pyrimidines.
  2. Ornithine carbamoyltransferase (EC) (OTCase) catalyzes the conversion of ornithine and carbamoyl phosphate to citrulline. In mammals this enzyme participates in the urea cycle [PUBMED:2662961] and is located in the mitochondrial matrix. In prokaryotes and eukaryotic microorganisms it is involved in the biosynthesis of arginine. In some bacterial species it is also involved in the degradation of arginine [PUBMED:3109911] (the arginine deaminase pathway).
It has been shown [PUBMED:6379651] that these two enzymes are evolutionary related. The predicted secondary structure of both enzymes are similar and there are some regions of sequence similarities. One of these regions includes three residues which have been shown, by crystallographic studies [PUBMED:6377306], to be implicated in binding the phosphoryl group of carbamoyl phosphate and is described by INTERPRO. The carboxyl-terminal, aspartate/ornithine-binding domain is connected to the amino-terminal domain by two alpha-helices, which comprise a hinge between domains [PUBMED:10318893].

Gene Ontology

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Domain organisation

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Alignments

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(4618)
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RP35
(1612)
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  Seed
(123)
Full
(10559)
Representative proteomes NCBI
(7158)
Meta
(4618)
RP15
(832)
RP35
(1612)
RP55
(2137)
RP75
(2543)
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  Seed
(123)
Full
(10559)
Representative proteomes NCBI
(7158)
Meta
(4618)
RP15
(832)
RP35
(1612)
RP55
(2137)
RP75
(2543)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

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External links

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Curation and family details

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Seed source: Prosite
Previous IDs: none
Type: Domain
Author: Finn RD, Griffiths-Jones SR
Number in seed: 123
Number in full: 10559
Average length of the domain: 158.00 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 43.70 %

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 29.4 29.4
Trusted cut-off 29.7 29.7
Noise cut-off 28.1 29.0
Model length: 158
Family (HMM) version: 19
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Species distribution

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Interactions

There are 3 interactions for this family. More...

PyrI_C OTCace OTCace_N

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 OTCace domain has been found. There are 296 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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