ARGI_MEDTR
ID ARGI_MEDTR Reviewed; 338 AA.
AC G7JFU5; A0A0C3WTP8;
DT 10-FEB-2021, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2014, sequence version 2.
DT 03-AUG-2022, entry version 59.
DE RecName: Full=Arginase, mitochondrial;
DE EC=3.5.3.1 {ECO:0000305|PubMed:32754173};
DE AltName: Full=Agmatinase ARGAH {ECO:0000305};
DE EC=3.5.3.11 {ECO:0000250|UniProtKB:P46637};
DE AltName: Full=Arginine amidohydrolase {ECO:0000305};
DE Short=MtARGAH {ECO:0000303|PubMed:32754173};
DE Flags: Precursor;
GN Name=ARGAH {ECO:0000303|PubMed:32754173};
GN OrderedLocusNames=MTR_4g024960 {ECO:0000312|EMBL:AES87366.2};
GN ORFNames=MtrunA17_Chr4g0011501 {ECO:0000312|EMBL:RHN59278.1};
OS Medicago truncatula (Barrel medic) (Medicago tribuloides).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade;
OC NPAAA clade; Hologalegina; IRL clade; Trifolieae; Medicago.
OX NCBI_TaxID=3880;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Jemalong A17;
RX PubMed=22089132; DOI=10.1038/nature10625;
RA Young N.D., Debelle F., Oldroyd G.E.D., Geurts R., Cannon S.B.,
RA Udvardi M.K., Benedito V.A., Mayer K.F.X., Gouzy J., Schoof H.,
RA Van de Peer Y., Proost S., Cook D.R., Meyers B.C., Spannagl M., Cheung F.,
RA De Mita S., Krishnakumar V., Gundlach H., Zhou S., Mudge J., Bharti A.K.,
RA Murray J.D., Naoumkina M.A., Rosen B., Silverstein K.A.T., Tang H.,
RA Rombauts S., Zhao P.X., Zhou P., Barbe V., Bardou P., Bechner M.,
RA Bellec A., Berger A., Berges H., Bidwell S., Bisseling T., Choisne N.,
RA Couloux A., Denny R., Deshpande S., Dai X., Doyle J.J., Dudez A.-M.,
RA Farmer A.D., Fouteau S., Franken C., Gibelin C., Gish J., Goldstein S.,
RA Gonzalez A.J., Green P.J., Hallab A., Hartog M., Hua A., Humphray S.J.,
RA Jeong D.-H., Jing Y., Jocker A., Kenton S.M., Kim D.-J., Klee K., Lai H.,
RA Lang C., Lin S., Macmil S.L., Magdelenat G., Matthews L., McCorrison J.,
RA Monaghan E.L., Mun J.-H., Najar F.Z., Nicholson C., Noirot C.,
RA O'Bleness M., Paule C.R., Poulain J., Prion F., Qin B., Qu C., Retzel E.F.,
RA Riddle C., Sallet E., Samain S., Samson N., Sanders I., Saurat O.,
RA Scarpelli C., Schiex T., Segurens B., Severin A.J., Sherrier D.J., Shi R.,
RA Sims S., Singer S.R., Sinharoy S., Sterck L., Viollet A., Wang B.-B.,
RA Wang K., Wang M., Wang X., Warfsmann J., Weissenbach J., White D.D.,
RA White J.D., Wiley G.B., Wincker P., Xing Y., Yang L., Yao Z., Ying F.,
RA Zhai J., Zhou L., Zuber A., Denarie J., Dixon R.A., May G.D.,
RA Schwartz D.C., Rogers J., Quetier F., Town C.D., Roe B.A.;
RT "The Medicago genome provides insight into the evolution of rhizobial
RT symbioses.";
RL Nature 480:520-524(2011).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Jemalong A17;
RX PubMed=24767513; DOI=10.1186/1471-2164-15-312;
RA Tang H., Krishnakumar V., Bidwell S., Rosen B., Chan A., Zhou S.,
RA Gentzbittel L., Childs K.L., Yandell M., Gundlach H., Mayer K.F.,
RA Schwartz D.C., Town C.D.;
RT "An improved genome release (version Mt4.0) for the model legume Medicago
RT truncatula.";
RL BMC Genomics 15:312-312(2014).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Jemalong A17;
RX PubMed=30397259; DOI=10.1038/s41477-018-0286-7;
RA Pecrix Y., Staton S.E., Sallet E., Lelandais-Briere C., Moreau S.,
RA Carrere S., Blein T., Jardinaud M.F., Latrasse D., Zouine M., Zahm M.,
RA Kreplak J., Mayjonade B., Satge C., Perez M., Cauet S., Marande W.,
RA Chantry-Darmon C., Lopez-Roques C., Bouchez O., Berard A., Debelle F.,
RA Munos S., Bendahmane A., Berges H., Niebel A., Buitink J., Frugier F.,
RA Benhamed M., Crespi M., Gouzy J., Gamas P.;
RT "Whole-genome landscape of Medicago truncatula symbiotic genes.";
RL Nat. Plants 4:1017-1025(2018).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.93 ANGSTROMS) IN COMPLEX WITH ORNITHINE AND
RP MANGANESE IONS, FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
RX PubMed=32754173; DOI=10.3389/fpls.2020.00987;
RA Sekula B.;
RT "The neighboring subunit is engaged to stabilize the substrate in the
RT active site of plant arginases.";
RL Front. Plant Sci. 11:987-987(2020).
CC -!- FUNCTION: Catalyzes the hydrolysis of L-arginine to urea and L-
CC ornithine (Probable). The latter can be utilized in the urea cycle or
CC as a precursor for the synthesis of both polyamines and proline
CC (Probable). Possesses agmatinase activity. Catalyzes the formation of
CC putrescine from agmatine (By similarity).
CC {ECO:0000250|UniProtKB:P46637, ECO:0000305,
CC ECO:0000305|PubMed:32754173}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + L-arginine = L-ornithine + urea; Xref=Rhea:RHEA:20569,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:16199, ChEBI:CHEBI:32682,
CC ChEBI:CHEBI:46911; EC=3.5.3.1;
CC Evidence={ECO:0000305|PubMed:32754173};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=agmatine + H2O = putrescine + urea; Xref=Rhea:RHEA:13929,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:16199, ChEBI:CHEBI:58145,
CC ChEBI:CHEBI:326268; EC=3.5.3.11;
CC Evidence={ECO:0000250|UniProtKB:P46637};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00742,
CC ECO:0000269|PubMed:32754173};
CC Note=Binds 2 manganese ions per subunit. {ECO:0000255|PROSITE-
CC ProRule:PRU00742, ECO:0000269|PubMed:32754173};
CC -!- PATHWAY: Nitrogen metabolism; urea cycle; L-ornithine and urea from L-
CC arginine: step 1/1. {ECO:0000305}.
CC -!- PATHWAY: Amine and polyamine biosynthesis; putrescine biosynthesis via
CC agmatine pathway; putrescine from agmatine: step 1/1. {ECO:0000305}.
CC -!- SUBUNIT: Forms homohexamers. {ECO:0000269|PubMed:32754173}.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000255}.
CC -!- SIMILARITY: Belongs to the arginase family. {ECO:0000255|PROSITE-
CC ProRule:PRU00742}.
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DR EMBL; CM001220; AES87366.2; -; Genomic_DNA.
DR EMBL; PSQE01000004; RHN59278.1; -; Genomic_DNA.
DR RefSeq; XP_003605169.2; XM_003605121.2.
DR PDB; 6VSS; X-ray; 1.93 A; A/B/C/D/E/F=1-338.
DR PDB; 6VST; X-ray; 2.12 A; A/B/C/D/E/F/G/H/I/J/K/L=1-338.
DR PDBsum; 6VSS; -.
DR PDBsum; 6VST; -.
DR AlphaFoldDB; G7JFU5; -.
DR SMR; G7JFU5; -.
DR STRING; 3880.AES87366; -.
DR EnsemblPlants; AES87366; AES87366; MTR_4g024960.
DR GeneID; 11420737; -.
DR Gramene; AES87366; AES87366; MTR_4g024960.
DR KEGG; mtr:MTR_4g024960; -.
DR eggNOG; KOG2964; Eukaryota.
DR HOGENOM; CLU_039478_3_0_1; -.
DR OrthoDB; 921352at2759; -.
DR UniPathway; UPA00158; UER00270.
DR UniPathway; UPA00534; UER00287.
DR Proteomes; UP000002051; Chromosome 4.
DR Proteomes; UP000265566; Chromosome 4.
DR ExpressionAtlas; G7JFU5; differential.
DR GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
DR GO; GO:0008783; F:agmatinase activity; IBA:GO_Central.
DR GO; GO:0004053; F:arginase activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019547; P:arginine catabolic process to ornithine; IDA:UniProtKB.
DR GO; GO:0034214; P:protein hexamerization; IDA:UniProtKB.
DR GO; GO:0033389; P:putrescine biosynthetic process from arginine, using agmatinase; IBA:GO_Central.
DR GO; GO:0000050; P:urea cycle; IEA:UniProtKB-UniPathway.
DR InterPro; IPR006035; Ureohydrolase.
DR InterPro; IPR023696; Ureohydrolase_dom_sf.
DR InterPro; IPR020855; Ureohydrolase_Mn_BS.
DR PANTHER; PTHR11358; PTHR11358; 1.
DR Pfam; PF00491; Arginase; 1.
DR PIRSF; PIRSF036979; Arginase; 1.
DR SUPFAM; SSF52768; SSF52768; 1.
DR PROSITE; PS01053; ARGINASE_1; 1.
DR PROSITE; PS51409; ARGINASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Arginine metabolism; Hydrolase; Manganese; Metal-binding;
KW Mitochondrion; Putrescine biosynthesis; Reference proteome;
KW Transit peptide.
FT TRANSIT 1..15
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 16..338
FT /note="Arginase, mitochondrial"
FT /id="PRO_0000451888"
FT BINDING 73
FT /ligand="L-ornithine"
FT /ligand_id="ChEBI:CHEBI:46911"
FT /evidence="ECO:0000269|PubMed:32754173"
FT BINDING 92..95
FT /ligand="L-ornithine"
FT /ligand_id="ChEBI:CHEBI:46911"
FT /evidence="ECO:0000269|PubMed:32754173"
FT BINDING 157
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00742,
FT ECO:0000269|PubMed:32754173"
FT BINDING 181
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00742,
FT ECO:0000269|PubMed:32754173"
FT BINDING 181
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00742,
FT ECO:0000269|PubMed:32754173"
FT BINDING 183
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00742,
FT ECO:0000269|PubMed:32754173"
FT BINDING 185..187
FT /ligand="L-ornithine"
FT /ligand_id="ChEBI:CHEBI:46911"
FT /evidence="ECO:0000269|PubMed:32754173"
FT BINDING 185
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00742,
FT ECO:0000269|PubMed:32754173"
FT BINDING 191..193
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P53608"
FT BINDING 220
FT /ligand="L-ornithine"
FT /ligand_id="ChEBI:CHEBI:46911"
FT /evidence="ECO:0000269|PubMed:32754173"
FT BINDING 266
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00742,
FT ECO:0000269|PubMed:32754173"
FT BINDING 266
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00742,
FT ECO:0000269|PubMed:32754173"
FT BINDING 268
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00742,
FT ECO:0000269|PubMed:32754173"
FT BINDING 309
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:32754173"
FT HELIX 22..54
FT /evidence="ECO:0007829|PDB:6VSS"
FT STRAND 58..66
FT /evidence="ECO:0007829|PDB:6VSS"
FT HELIX 77..80
FT /evidence="ECO:0007829|PDB:6VSS"
FT HELIX 81..90
FT /evidence="ECO:0007829|PDB:6VSS"
FT TURN 107..109
FT /evidence="ECO:0007829|PDB:6VSS"
FT STRAND 110..115
FT /evidence="ECO:0007829|PDB:6VSS"
FT HELIX 118..122
FT /evidence="ECO:0007829|PDB:6VSS"
FT TURN 123..125
FT /evidence="ECO:0007829|PDB:6VSS"
FT HELIX 128..143
FT /evidence="ECO:0007829|PDB:6VSS"
FT STRAND 148..156
FT /evidence="ECO:0007829|PDB:6VSS"
FT HELIX 157..159
FT /evidence="ECO:0007829|PDB:6VSS"
FT HELIX 160..171
FT /evidence="ECO:0007829|PDB:6VSS"
FT STRAND 175..180
FT /evidence="ECO:0007829|PDB:6VSS"
FT HELIX 200..206
FT /evidence="ECO:0007829|PDB:6VSS"
FT STRAND 210..218
FT /evidence="ECO:0007829|PDB:6VSS"
FT HELIX 223..232
FT /evidence="ECO:0007829|PDB:6VSS"
FT STRAND 235..238
FT /evidence="ECO:0007829|PDB:6VSS"
FT HELIX 239..241
FT /evidence="ECO:0007829|PDB:6VSS"
FT HELIX 242..249
FT /evidence="ECO:0007829|PDB:6VSS"
FT STRAND 261..266
FT /evidence="ECO:0007829|PDB:6VSS"
FT HELIX 267..269
FT /evidence="ECO:0007829|PDB:6VSS"
FT TURN 272..274
FT /evidence="ECO:0007829|PDB:6VSS"
FT STRAND 277..279
FT /evidence="ECO:0007829|PDB:6VST"
FT HELIX 288..297
FT /evidence="ECO:0007829|PDB:6VSS"
FT STRAND 302..308
FT /evidence="ECO:0007829|PDB:6VSS"
FT HELIX 312..314
FT /evidence="ECO:0007829|PDB:6VSS"
FT HELIX 320..336
FT /evidence="ECO:0007829|PDB:6VSS"
SQ SEQUENCE 338 AA; 37199 MW; 4A88C96D0EC88B07 CRC64;
MSTIARRGFH YMQRLNSANV SPALLEKAQN RVIDAALTFI RERAKFKGEL MRSLGGVAAT
SSLLGVPLGH HSSFHEGSAF APPRIREAIW CDSTNSTTEE GKNLRDPRVI TNVGDVPIEE
IRDCGVDDKR LANVISESVK LVMDEDPLRP LVLGGDHSIS FPVVRAVSEK LGGAVDILHF
DAHPDLYHDF EGNYYSHASP FARIMEGGYA RRLVQVGIRS ITNDVREQVK KYGVETHEMR
TLSRDRPILE NLKLGEGVKG VYVSIDVDSL DPSIAPGVSH HEPGGLLFRD ILNILQNLQG
DIVGGDVVEY NPQRDTYDGI TALVAAKLVR ELAAKMSK
