AGUA_MEDTR
ID AGUA_MEDTR Reviewed; 374 AA.
AC G7JT50; A0A0C3X550; B7FI21; I3S1J5;
DT 17-JUN-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2014, sequence version 2.
DT 03-AUG-2022, entry version 54.
DE RecName: Full=Agmatine deiminase {ECO:0000305};
DE EC=3.5.3.12 {ECO:0000250|UniProtKB:Q8GWW7};
DE AltName: Full=Agmatine iminohydrolase {ECO:0000303|PubMed:30984210};
DE Short=MtAIH {ECO:0000303|PubMed:30984210};
GN Name=AIH {ECO:0000303|PubMed:30984210};
GN OrderedLocusNames=MTR_4g112810 {ECO:0000312|EMBL:AES91372.2};
GN ORFNames=MtrunA17_Chr4g0061951 {ECO:0000312|EMBL:RHN63774.1};
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Moskal W., Chan A., Cheung F., Xiao Y., Town C.D.;
RT "Medicago truncatula full length cdna cloning project.";
RL Submitted (DEC-2008) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.20 ANGSTROMS) OF 11-374 IN COMPLEX WITH AGMATINE,
RP AND SUBUNIT.
RX PubMed=30984210; DOI=10.3389/fpls.2019.00320;
RA Sekula B., Dauter Z.;
RT "Structural study of agmatine iminohydrolase from Medicago truncatula, the
RT second enzyme of the agmatine route of putrescine biosynthesis in plants.";
RL Front. Plant Sci. 10:320-320(2019).
CC -!- FUNCTION: Mediates the hydrolysis of agmatine into N-
CC carbamoylputrescine in the arginine decarboxylase (ADC) pathway of
CC putrescine biosynthesis, a basic polyamine.
CC {ECO:0000250|UniProtKB:Q8GWW7}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=agmatine + H2O = N-carbamoylputrescine + NH4(+);
CC Xref=Rhea:RHEA:18037, ChEBI:CHEBI:15377, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:58145, ChEBI:CHEBI:58318; EC=3.5.3.12;
CC Evidence={ECO:0000250|UniProtKB:Q8GWW7};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:18038;
CC Evidence={ECO:0000250|UniProtKB:Q8GWW7};
CC -!- PATHWAY: Amine and polyamine biosynthesis; putrescine biosynthesis via
CC agmatine pathway; N-carbamoylputrescine from agmatine: step 1/1.
CC {ECO:0000305}.
CC -!- SUBUNIT: Forms homodimers. {ECO:0000269|PubMed:30984210}.
CC -!- SIMILARITY: Belongs to the agmatine deiminase family. {ECO:0000305}.
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DR EMBL; CM001220; AES91372.2; -; Genomic_DNA.
DR EMBL; PSQE01000004; RHN63774.1; -; Genomic_DNA.
DR EMBL; BT051738; ACJ84400.1; -; mRNA.
DR EMBL; BT134342; AFK34137.1; -; mRNA.
DR RefSeq; XP_003609175.2; XM_003609127.2.
DR PDB; 6NIB; X-ray; 1.20 A; A=11-374.
DR PDB; 6NIC; X-ray; 2.20 A; A/B/C/D=11-374.
DR PDBsum; 6NIB; -.
DR PDBsum; 6NIC; -.
DR AlphaFoldDB; G7JT50; -.
DR SMR; G7JT50; -.
DR STRING; 3880.AES91372; -.
DR EnsemblPlants; AES91372; AES91372; MTR_4g112810.
DR GeneID; 11445422; -.
DR Gramene; AES91372; AES91372; MTR_4g112810.
DR KEGG; mtr:MTR_4g112810; -.
DR eggNOG; ENOG502QUHM; Eukaryota.
DR HOGENOM; CLU_037682_1_0_1; -.
DR OrthoDB; 636636at2759; -.
DR UniPathway; UPA00534; UER00285.
DR Proteomes; UP000002051; Chromosome 4.
DR Proteomes; UP000265566; Chromosome 4.
DR ExpressionAtlas; G7JT50; differential.
DR GO; GO:0047632; F:agmatine deiminase activity; IEA:UniProtKB-EC.
DR GO; GO:0004668; F:protein-arginine deiminase activity; IEA:InterPro.
DR GO; GO:0033388; P:putrescine biosynthetic process from arginine; IEA:UniProtKB-UniPathway.
DR HAMAP; MF_01841; Agmatine_deimin; 1.
DR InterPro; IPR017754; Agmatine_deiminase.
DR InterPro; IPR007466; Peptidyl-Arg-deiminase_porph.
DR PANTHER; PTHR31377; PTHR31377; 1.
DR Pfam; PF04371; PAD_porph; 1.
DR TIGRFAMs; TIGR03380; agmatine_aguA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Polyamine biosynthesis; Reference proteome.
FT CHAIN 1..374
FT /note="Agmatine deiminase"
FT /id="PRO_0000450243"
FT ACT_SITE 366
FT /note="Amidino-cysteine intermediate"
FT /evidence="ECO:0000250|UniProtKB:Q837U5"
FT BINDING 220
FT /ligand="agmatine"
FT /ligand_id="ChEBI:CHEBI:58145"
FT /evidence="ECO:0000269|PubMed:30984210,
FT ECO:0007744|PDB:6NIC"
FT BINDING 226
FT /ligand="agmatine"
FT /ligand_id="ChEBI:CHEBI:58145"
FT /evidence="ECO:0000269|PubMed:30984210,
FT ECO:0007744|PDB:6NIC"
FT CONFLICT 102
FT /note="R -> G (in Ref. 4; ACJ84400/AFK34137)"
FT /evidence="ECO:0000305"
FT CONFLICT 150
FT /note="E -> G (in Ref. 4; ACJ84400/AFK34137)"
FT /evidence="ECO:0000305"
FT CONFLICT 340
FT /note="S -> F (in Ref. 4; AFK34137)"
FT /evidence="ECO:0000305"
FT STRAND 22..27
FT /evidence="ECO:0007829|PDB:6NIB"
FT TURN 33..35
FT /evidence="ECO:0007829|PDB:6NIB"
FT HELIX 37..40
FT /evidence="ECO:0007829|PDB:6NIB"
FT HELIX 41..55
FT /evidence="ECO:0007829|PDB:6NIB"
FT STRAND 58..64
FT /evidence="ECO:0007829|PDB:6NIB"
FT HELIX 66..68
FT /evidence="ECO:0007829|PDB:6NIB"
FT HELIX 69..75
FT /evidence="ECO:0007829|PDB:6NIB"
FT STRAND 80..84
FT /evidence="ECO:0007829|PDB:6NIB"
FT HELIX 92..95
FT /evidence="ECO:0007829|PDB:6NIB"
FT STRAND 98..101
FT /evidence="ECO:0007829|PDB:6NIB"
FT STRAND 115..121
FT /evidence="ECO:0007829|PDB:6NIB"
FT TURN 124..126
FT /evidence="ECO:0007829|PDB:6NIB"
FT HELIX 127..130
FT /evidence="ECO:0007829|PDB:6NIC"
FT HELIX 137..150
FT /evidence="ECO:0007829|PDB:6NIB"
FT STRAND 154..160
FT /evidence="ECO:0007829|PDB:6NIB"
FT HELIX 163..165
FT /evidence="ECO:0007829|PDB:6NIB"
FT STRAND 166..168
FT /evidence="ECO:0007829|PDB:6NIB"
FT STRAND 170..177
FT /evidence="ECO:0007829|PDB:6NIB"
FT HELIX 178..181
FT /evidence="ECO:0007829|PDB:6NIB"
FT TURN 184..186
FT /evidence="ECO:0007829|PDB:6NIB"
FT HELIX 192..203
FT /evidence="ECO:0007829|PDB:6NIB"
FT STRAND 206..212
FT /evidence="ECO:0007829|PDB:6NIB"
FT TURN 219..222
FT /evidence="ECO:0007829|PDB:6NIB"
FT HELIX 225..227
FT /evidence="ECO:0007829|PDB:6NIB"
FT STRAND 229..233
FT /evidence="ECO:0007829|PDB:6NIB"
FT STRAND 236..241
FT /evidence="ECO:0007829|PDB:6NIB"
FT HELIX 249..260
FT /evidence="ECO:0007829|PDB:6NIB"
FT STRAND 272..277
FT /evidence="ECO:0007829|PDB:6NIB"
FT HELIX 286..290
FT /evidence="ECO:0007829|PDB:6NIB"
FT STRAND 296..298
FT /evidence="ECO:0007829|PDB:6NIC"
FT STRAND 315..317
FT /evidence="ECO:0007829|PDB:6NIB"
FT STRAND 320..324
FT /evidence="ECO:0007829|PDB:6NIB"
FT HELIX 329..342
FT /evidence="ECO:0007829|PDB:6NIB"
FT STRAND 346..351
FT /evidence="ECO:0007829|PDB:6NIB"
FT TURN 352..354
FT /evidence="ECO:0007829|PDB:6NIB"
FT HELIX 355..358
FT /evidence="ECO:0007829|PDB:6NIB"
FT TURN 359..361
FT /evidence="ECO:0007829|PDB:6NIB"
FT HELIX 364..367
FT /evidence="ECO:0007829|PDB:6NIB"
FT STRAND 368..372
FT /evidence="ECO:0007829|PDB:6NIB"
SQ SEQUENCE 374 AA; 42126 MW; CA27F9387E4EC21C CRC64;
MMHLENTPTF HGFHMPAEWE PHSQCWIGWP ERADNWRDGA VHAQLVFTRV AAAISRFEKV
TVCASSAQWE NARNQLPDHV RVVEISSNDS WFRDIGPTFV VRRETSKSDD AEHRIAGIDW
TFNSWGGLED GCYCDWSLDS LVKKKILDVE RIPRFSHSMV LEGGSIHVDG EGTCITTEEC
LLNKNRNPHL SKSQIEDELK AYLGVRKVIW LPRGLYGDDD TNGHVDNMCC FVRPGAVLLS
WTDDKTDPQY ERSEEAYSLF SSVTDANGRK FEVIKLHVPG PLYMTEKEAA GVFQDDGAKP
RLPGTRLAAS YVNFYIANGA IIAPQFGDKK WDDEAIRVLS KTFPHHEVVG IEGSREIVLS
GGNIHCITQQ QPAI
