PROSITE documentation PDOC00135

Arginase family signature and profile

Description

Arginase family proteins are ureohydrolases with important roles in arginine/agmatine metabolism, the urea cycle, histidine degradation, and other pathways. The family includes arginase and evolutionary related [1] enzymes of about 300 amino acids that typically contain two manganese ions in the active site.

Some proteins that belong to the arginase family are listed below:

  • Arginase (EC 3.5.3.1), a ubiquitous enzyme which catalyzes the degradation of arginine to ornithine and urea [2]. Two isoenzymes are found in mammals. Arginase-1 catalyzes the final cytosolic step of the urea cycle in liver, but it is also found in non-hepatic tissues. Arginase-2 is a mitochondrial enzyme that functions in arginine homeostasis in nonhepatic tissues. Deficiency of arginase can lead to diseases related to the accumulation of arginine or ammonia.
  • Agmatinase (EC 3.5.3.11) (agmatine ureohydrolase), a prokaryotic enzyme (gene speB) that catalyzes the hydrolysis of agmatine into putrescine and urea.
  • Formiminoglutamase (EC 3.5.3.8) (formiminoglutamate hydrolase), a prokaryotic enzyme (gene hutG) that hydrolyzes N-formimino-glutamate into glutamate and formamide.
  • Proclavaminate amidinohydrolase (EC 3.5.3.22) from Streptomyces clavuligerus (gene pah), an enzyme involved in antibiotic clavulanic acid biosynthesis.
  • Guanidinobutyrase (EC 3.5.3.7) from Arthrobacter sp. (gene gbh), an enzyme that hydrolyzes guanidinobutanoate into aminobutanoate and urea and that requires one zinc ion instead of manganese.
  • Hypothetical proteins from methanogenic archaebacteria.

Known 3-D structures of such enzymes show trimeric or hexameric structures [3,4,5,6]. Each monomer forms a conserved α/β fold with a central parallel β-sheet flanked on both sides by several α-helices (see <PDB:1RLA; B>). Three conserved regions that contain charged residues which are involved in the binding of the two manganese ions in the active site are located in loop segments of the central β-sheet [3,4,5,6]. We have used one of these regions for a signature pattern and we have also developed a profile that covers the entire arginase structure.

Expert(s) to contact by email:

Ouzounis C.

Last update:

November 2008 / Text revised; profile added; patterns deleted.

Technical section

PROSITE methods (with tools and information) covered by this documentation:

ARGINASE_2, PS51409Arginase family profile  (MATRIX)
Sequences known to belong to this class detected by the profile: ALL
Other sequence(s) detected in Swiss-Prot: NONE.
Domain architecture view of Swiss-Prot proteins matching PS51409
PS51409
• Retrieve an alignment of Swiss-Prot true positive hits:
  Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format
Retrieve the sequence logo from the alignment
Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS51409
Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS51409
Scan Swiss-Prot/TrEMBL entries against PS51409
view ligand binding statistics
Matching PDB structures: 1CEV 1D3V 1GQ6 1GQ7 ... [ALL]
ARGINASE_1, PS01053Arginase family signature  (PATTERN)
Consensus pattern: [ST]-[LIVMFY]-D-[LIVM]-D-x(3)-[PAQ]-x(3)-P-[GSA]-x(7)-G
The 2 D's bind manganese
Sequences known to belong to this class detected by the pattern: ALL
Other sequence(s) detected in Swiss-Prot: NONE.
• Retrieve an alignment of Swiss-Prot true positive hits:
  Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format
Retrieve the sequence logo from the alignment
Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS01053
Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS01053
Scan Swiss-Prot/TrEMBL entries against PS01053
view ligand binding statistics
Matching PDB structures: 1CEV 1D3V 1GQ6 1GQ7 ... [ALL]

References

1 Authors Ouzounis C.A., Kyrpides N.C.
Title On the evolution of arginases and related enzymes.
Source J. Mol. Evol. 39:101-104(1994).
PubMed ID 8064866
2 Authors Jenkinson C.P., Grody W.W., Cederbaum S.D.
Title Comparative properties of arginases.
Source Comp. Biochem. Physiol. 114B:107-132(1996).
PubMed ID 8759304
3 Authors Kanyo Z.F., Scolnick L.R., Ash D.E., Christianson D.W.
Title Structure of a unique binuclear manganese cluster in arginase.
Source Nature 383:554-557(1996).
PubMed ID 8849731
4 Authors Elkins J.M., Clifton I.J., Hernandez H., Doan L.X., Robinson C.V., Schofield C.J., Hewitson K.S.
Title Oligomeric structure of proclavaminic acid amidino hydrolase: evolution of a hydrolytic enzyme in clavulanic acid biosynthesis.
Source Biochem. J. 366:423-434(2002).
PubMed ID 12020346
DOI 10.1042/BJ20020125
5 Authors Ahn H.J., Kim K.H., Lee J., Ha J.Y., Lee H.H., Kim D., Yoon H.J., Kwon A.R., Suh S.W.
Title Crystal structure of agmatinase reveals structural conservation and inhibition mechanism of the ureohydrolase superfamily.
Source J. Biol. Chem. 279:50505-50513(2004).
PubMed ID 15355972
DOI 10.1074/jbc.M409246200
6 Authors Dowling D.P., Di Costanzo L., Gennadios H.A., Christianson D.W.
Title Evolution of the arginase fold and functional diversity.
Source Cell. Mol. Life Sci. 65:2039-2055(2008).
PubMed ID 18360740
DOI 10.1007/s00018-008-7554-z

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