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 | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 the pala-liganded aspartate transcarbamoylase catalytic subunit from pyrococcus abyssi | |||||||||
| Identifiers | |||||||||
| Symbol | OTCace_N | ||||||||
| Pfam | PF02729 | ||||||||
| InterPro | IPR006132 | ||||||||
| PROSITE | PDOC00091 | ||||||||
| SCOPe | 1raa / SUPFAM | ||||||||
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| Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | OTCace | ||||||||
| Pfam | PF00185 | ||||||||
| SCOPe | 1raa / SUPFAM | ||||||||
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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
- ^ 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". Proceedings of the National Academy of Sciences, USA. 81 (15): 4864–4868. doi:10.1073/pnas.81.15.4864. PMC 391592. PMID 6379651.
- ^ Ke HM, Honzatko RB, Lipscomb WN (July 1984). "Structure of unligated aspartate carbamoyltransferase of Escherichia coli at 2.6-A resolution". Proceedings of the National Academy of Sciences, USA. 81 (13): 4037–4040. doi:10.1073/pnas.81.13.4037. PMC 345363. PMID 6377306.
- ^ 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". Proceedings of the National Academy of Sciences, USA. 96 (10): 5388–5393. doi:10.1073/pnas.96.10.5388. PMC 21869. PMID 10318893.
- ^ Lerner CG, Switzer RL (August 1986). "Cloning and structure of the Bacillus subtilis aspartate transcarbamylase gene (pyrB)". Journal of Biological Chemistry. 261 (24): 11156–11165. PMID 3015959.
- ^ 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): 157–164. doi:10.1002/bies.950150303. PMID 8098212.
- ^ Takiguchi M, Matsubasa T, Amaya Y, Mori M (May 1989). "Evolutionary aspects of urea cycle enzyme genes". BioEssays. 10 (5): 163–186. doi:10.1002/bies.950100506. PMID 2662961.
- ^ 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". European Journal of Biochemistry. 166 (1): 111–117. doi:10.1111/j.1432-1033.1987.tb13489.x. PMID 3109911.
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Literature references
-
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
| Similarity to PfamA using HHSearch: | F420_oxidored |
External database links
| HOMSTRAD: | OTCace |
| PRINTS: | PR00101 |
| PROSITE: | PDOC00091 |
| SCOP: | 1raa |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006131
This family contains two related enzymes:
- 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.
- 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).
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
| Molecular function | carboxyl- or carbamoyltransferase activity (GO:0016743) |
| amino acid binding (GO:0016597) | |
| Biological process | cellular amino acid metabolic process (GO:0006520) |
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 Asp-glut_race (CL0399), which has the following description:
Superfamily contains aspartate racemase, glutamate racemase, hydantoin racemase and arylmalonate decarboxylase families from fungi, plants, bacteria and archaeal species.
The clan contains the following 5 members:
Amdase AroM Asp_Glu_race Asp_Glu_race_2 OTCaceAlignments
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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| Seed (50) |
Full (17730) |
Representative proteomes | UniProt (50167) |
NCBI (58879) |
Meta (4401) |
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| RP15 (4487) |
RP35 (11690) |
RP55 (17632) |
RP75 (24998) |
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| PP/heatmap | 1 | ||||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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| Seed (50) |
Full (17730) |
Representative proteomes | UniProt (50167) |
NCBI (58879) |
Meta (4401) |
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|---|---|---|---|---|---|---|---|---|---|
| RP15 (4487) |
RP35 (11690) |
RP55 (17632) |
RP75 (24998) |
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| Raw Stockholm | |||||||||
| Gzipped | |||||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
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: | Prosite |
| Previous IDs: | none |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Finn RD  , Griffiths-Jones SR
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| Number in seed: | 50 |
| Number in full: | 17730 |
| Average length of the domain: | 154.00 aa |
| Average identity of full alignment: | 28 % |
| Average coverage of the sequence by the domain: | 38.11 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 157 | ||||||||||||
| Family (HMM) version: | 24 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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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 371 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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