Summary: Arginase family
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This is the Wikipedia entry entitled "Ureohydrolase". More...
Ureohydrolase Edit Wikipedia article
Ureohydrolase | |||||||||||
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Identifiers | |||||||||||
Symbol | Ureohydrolase | ||||||||||
Pfam | PF00491 | ||||||||||
InterPro | IPR006035 | ||||||||||
PROSITE | PDOC00135 | ||||||||||
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A ureohydrolase is a type of hydrolase enzyme.[1]
The ureohydrolase superfamily includes arginase (EC 3.5.3.1), agmatinase (EC 3.5.3.11), formiminoglutamase (EC 3.5.3.8) and proclavaminate amidinohydrolase (EC 3.5.3.22).[2] These enzymes share a 3-layer alpha-beta-alpha structure,[2][3][4] and play important roles in arginine/agmatine metabolism, the urea cycle, histidine degradation, and other pathways.
Arginase, which catalyses the conversion of arginine to urea and ornithine, is one of the five members of the urea cycle enzymes that convert ammonia to urea as the principal product of nitrogen excretion.[5] There are several arginase isozymes that differ in catalytic, molecular and immunological properties. Deficiency in the liver isozyme leads to argininemia, which is usually associated with hyperammonemia.
Agmatinase hydrolyses agmatine to putrescine, the precursor for the biosynthesis of higher polyamines, spermidine and spermine. In addition, agmatine may play an important regulatory role in mammals.[6]
Formiminoglutamase catalyses the fourth step in histidine degradation, acting to hydrolyse N-formimidoyl-L-glutamate to L-glutamate and formamide.
Proclavaminate amidinohydrolase is involved in clavulanic acid biosynthesis. Clavulanic acid acts as an inhibitor of a wide range of beta-lactamase enzymes that are used by various microorganisms to resist beta-lactam antibiotics. As a result, this enzyme improves the effectiveness of beta-lactamase antibiotics.[4][7]
References
- ^ Ureohydrolases at the US National Library of Medicine Medical Subject Headings (MeSH)
- ^ a b Lee J, Suh SW, Kim KH, Kim D, Yoon HJ, Kwon AR, Ahn HJ, Ha JY, Lee HH (2004). "Crystal structure of agmatinase reveals structural conservation and inhibition mechanism of the ureohydrolase superfamily". J. Biol. Chem. 279 (48): 50505–13. doi:10.1074/jbc.M409246200. PMID 15355972.
- ^ Christianson DW, Di Costanzo L, Sabio G, Mora A, Rodriguez PC, Ochoa AC, Centeno F (2005). "Crystal structure of human arginase I at 1.29-A resolution and exploration of inhibition in the immune response". Proc. Natl. Acad. Sci. U.S.A. 102 (37): 13058–13063. doi:10.1073/pnas.0504027102. PMC 1201588. PMID 16141327.
- ^ a b Clifton IJ, Elkins JM, Hernandez H (2002). "Oligomeric structure of proclavaminic acid amidino hydrolase: evolution of a hydrolytic enzyme in clavulanic acid biosynthesis". Biochem. J. 366 (Pt 2): 423. doi:10.1042/BJ20020125. PMC 1222790. PMID 12020346.
- ^ Baker BS, Tata JR, Xu Q (1993). "Developmental and hormonal regulation of the Xenopus liver-type arginase gene". Eur. J. Biochem. 211 (3): 891–898. doi:10.1111/j.1432-1033.1993.tb17622.x. PMID 7916684.
- ^ Ahn HJ, Kim KH, Lee J, et al. (November 2004). "Crystal structure of agmatinase reveals structural conservation and inhibition mechanism of the ureohydrolase superfamily". J. Biol. Chem. 279 (48): 50505–13. doi:10.1074/jbc.M409246200. PMID 15355972.
- ^ "IPR006035 Ureohydrolase". Retrieved 2009-02-17.
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Arginase family Provide feedback
No Pfam abstract.
External database links
HOMSTRAD: | arginase |
PROSITE: | PDOC00135 |
SCOP: | 1rla |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006035
The ureohydrolase superfamily includes arginase (EC), agmatinase (EC), formiminoglutamase (EC) and proclavaminate amidinohydrolase (EC) [PUBMED:15355972]. These enzymes share a 3-layer alpha-beta-alpha structure [PUBMED:15355972, PUBMED:16141327, PUBMED:12020346], and play important roles in arginine/agmatine metabolism, the urea cycle, histidine degradation, and other pathways.
Arginase, which catalyses the conversion of arginine to urea and ornithine, is one of the five members of the urea cycle enzymes that convert ammonia to urea as the principal product of nitrogen excretion [PUBMED:7916684]. There are several arginase isozymes that differ in catalytic, molecular and immunological properties. Deficiency in the liver isozyme leads to argininemia, which is usually associated with hyperammonemia.
Agmatinase hydrolyses agmatine to putrescine, the precursor for the biosynthesis of higher polyamines, spermidine and spermine. In addition, agmatine may play an important regulatory role in mammals.
Formiminoglutamase catalyses the fourth step in histidine degradation, acting to hydrolyse N-formimidoyl-L-glutamate to L-glutamate and formamide.
Proclavaminate amidinohydrolase is involved in clavulanic acid biosynthesis. Clavulanic acid acts as an inhibitor of a wide range of beta-lactamase enzymes that are used by various microorganisms to resist beta-lactam antibiotics. As a result, this enzyme improves the effectiveness of beta-lactamase antibiotics [PUBMED:12020346].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | metal ion binding (GO:0046872) |
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 Arginase (CL0302), which has the following description:
This superfamily includes arginase enzymes as well as histone deacetylases and related enzymes [1].
The clan contains the following 3 members:
Arginase Hist_deacetyl UPF0489Alignments
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 (227) |
Full (13691) |
Representative proteomes | UniProt (54920) |
NCBI (73011) |
Meta (4142) |
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RP15 (1495) |
RP35 (5745) |
RP55 (12680) |
RP75 (22193) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (227) |
Full (13691) |
Representative proteomes | UniProt (54920) |
NCBI (73011) |
Meta (4142) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (1495) |
RP35 (5745) |
RP55 (12680) |
RP75 (22193) |
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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: | arginase; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 227 |
Number in full: | 13691 |
Average length of the domain: | 271.70 aa |
Average identity of full alignment: | 24 % |
Average coverage of the sequence by the domain: | 83.49 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 280 | ||||||||||||
Family (HMM) version: | 22 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There is 1 interaction for this family. More...
ArginaseStructures
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 Arginase domain has been found. There are 411 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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