AGUA_ARATH
ID AGUA_ARATH Reviewed; 383 AA.
AC Q8GWW7; Q94IC7; Q9LEZ0;
DT 16-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT 16-AUG-2005, sequence version 2.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=Agmatine deiminase;
DE EC=3.5.3.12 {ECO:0000269|PubMed:12782327, ECO:0000269|PubMed:12914918};
DE AltName: Full=Agmatine iminohydrolase;
DE AltName: Full=Protein EMBRYO DEFECTIVE 1873;
GN Name=AIH; Synonyms=EMB1873; OrderedLocusNames=At5g08170;
GN ORFNames=T22D6.110;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 5-383.
RA Kimura K., Nakada Y., Itoh Y.;
RT "Partial Arabidopsis thaliana cDNA encoding a protein of unknown
RT function.";
RL Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT,
RP ACTIVITY REGULATION, AND MUTAGENESIS OF CYS-180; CYS-229; CYS-230 AND
RP CYS-366.
RX PubMed=12782327; DOI=10.1016/s0014-5793(03)00515-5;
RA Janowitz T., Kneifel H., Piotrowski M.;
RT "Identification and characterization of plant agmatine iminohydrolase, the
RT last missing link in polyamine biosynthesis of plants.";
RL FEBS Lett. 544:258-261(2003).
RN [7]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=12914918; DOI=10.1016/s0014-5793(03)00756-7;
RA Illingworth C., Mayer M.J., Elliott K., Hanfrey C., Walton N.J.,
RA Michael A.J.;
RT "The diverse bacterial origins of the Arabidopsis polyamine biosynthetic
RT pathway.";
RL FEBS Lett. 549:26-30(2003).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.53 ANGSTROMS) OF 2-383.
RA Wesenberg G.E., Smith D.W., Phillips G.N. Jr., Bingman C.A., Allard S.T.M.;
RT "X-ray structure of gene product from Arabidopsis thaliana At5g08170,
RT agmatine iminohydrolase.";
RL Submitted (AUG-2004) to the PDB data bank.
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.53 ANGSTROMS), AND SUBUNIT.
RX PubMed=17850744; DOI=10.1016/j.str.2007.06.019;
RA Levin E.J., Kondrashov D.A., Wesenberg G.E., Phillips G.N. Jr.;
RT "Ensemble refinement of protein crystal structures: validation and
RT application.";
RL Structure 15:1040-1052(2007).
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:0000305|PubMed:12782327, ECO:0000305|PubMed:12914918}.
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:0000269|PubMed:12782327, ECO:0000269|PubMed:12914918};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:18038;
CC Evidence={ECO:0000269|PubMed:12782327, ECO:0000269|PubMed:12914918};
CC -!- ACTIVITY REGULATION: Inhibited by N-ethylmaleimide and iodoacetamide.
CC {ECO:0000269|PubMed:12782327}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Vmax=112 nmol/sec/mg enzyme with agmatine as substrate
CC {ECO:0000269|PubMed:12782327};
CC pH dependence:
CC Optimum pH is 7.0. {ECO:0000269|PubMed:12782327};
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:12782327,
CC ECO:0000269|PubMed:17850744}.
CC -!- SIMILARITY: Belongs to the agmatine deiminase family. {ECO:0000305}.
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DR EMBL; AL357612; CAB93718.1; -; Genomic_DNA.
DR EMBL; CP002688; AED91261.1; -; Genomic_DNA.
DR EMBL; AK118589; BAC43189.1; -; mRNA.
DR EMBL; BT005341; AAO63405.1; -; mRNA.
DR EMBL; AB062682; BAB59127.1; -; mRNA.
DR PIR; T50502; T50502.
DR RefSeq; NP_196434.1; NM_120900.6.
DR PDB; 1VKP; X-ray; 1.53 A; A/B=1-383.
DR PDB; 2Q3U; X-ray; 1.53 A; A/B=1-383.
DR PDB; 3H7C; X-ray; 1.50 A; X=2-383.
DR PDB; 3H7K; X-ray; 1.84 A; A=2-383.
DR PDBsum; 1VKP; -.
DR PDBsum; 2Q3U; -.
DR PDBsum; 3H7C; -.
DR PDBsum; 3H7K; -.
DR AlphaFoldDB; Q8GWW7; -.
DR SMR; Q8GWW7; -.
DR STRING; 3702.AT5G08170.1; -.
DR iPTMnet; Q8GWW7; -.
DR PaxDb; Q8GWW7; -.
DR PRIDE; Q8GWW7; -.
DR ProteomicsDB; 244936; -.
DR DNASU; 830713; -.
DR EnsemblPlants; AT5G08170.1; AT5G08170.1; AT5G08170.
DR GeneID; 830713; -.
DR Gramene; AT5G08170.1; AT5G08170.1; AT5G08170.
DR KEGG; ath:AT5G08170; -.
DR Araport; AT5G08170; -.
DR TAIR; locus:2181499; AT5G08170.
DR eggNOG; ENOG502QUHM; Eukaryota.
DR HOGENOM; CLU_037682_1_0_1; -.
DR InParanoid; Q8GWW7; -.
DR OMA; WCRDHGP; -.
DR OrthoDB; 636636at2759; -.
DR PhylomeDB; Q8GWW7; -.
DR BioCyc; MetaCyc:MON-2641; -.
DR UniPathway; UPA00534; UER00285.
DR EvolutionaryTrace; Q8GWW7; -.
DR PRO; PR:Q8GWW7; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8GWW7; baseline and differential.
DR Genevisible; Q8GWW7; AT.
DR GO; GO:0047632; F:agmatine deiminase activity; IDA:TAIR.
DR GO; GO:0004668; F:protein-arginine deiminase activity; IEA:InterPro.
DR GO; GO:0006596; P:polyamine biosynthetic process; IDA:TAIR.
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..383
FT /note="Agmatine deiminase"
FT /id="PRO_0000194350"
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:0000250|UniProtKB:G7JT50"
FT BINDING 226
FT /ligand="agmatine"
FT /ligand_id="ChEBI:CHEBI:58145"
FT /evidence="ECO:0000250|UniProtKB:G7JT50"
FT MUTAGEN 180
FT /note="C->A: Impairs enzyme activity but does not abolish
FT it."
FT /evidence="ECO:0000269|PubMed:12782327"
FT MUTAGEN 229
FT /note="C->A: No effect."
FT /evidence="ECO:0000269|PubMed:12782327"
FT MUTAGEN 230
FT /note="C->A: No effect."
FT /evidence="ECO:0000269|PubMed:12782327"
FT MUTAGEN 366
FT /note="C->A: Impairs enzyme activity but does not abolish
FT it."
FT /evidence="ECO:0000269|PubMed:12782327"
FT CONFLICT 49
FT /note="D -> G (in Ref. 3; BAC43189 and 4; AAO63405)"
FT /evidence="ECO:0000305"
FT CONFLICT 59
FT /note="P -> L (in Ref. 5; BAB59127)"
FT /evidence="ECO:0000305"
FT CONFLICT 126
FT /note="G -> V (in Ref. 5; BAB59127)"
FT /evidence="ECO:0000305"
FT HELIX 9..11
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 22..27
FT /evidence="ECO:0007829|PDB:3H7C"
FT TURN 33..35
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 38..40
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 41..55
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 60..64
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 66..68
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 69..75
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 80..84
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 92..95
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 98..101
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 114..121
FT /evidence="ECO:0007829|PDB:3H7C"
FT TURN 124..126
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 127..130
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 139..141
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 142..150
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 154..160
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 163..165
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 166..168
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 170..177
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 178..181
FT /evidence="ECO:0007829|PDB:3H7C"
FT TURN 184..186
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 192..203
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 207..212
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 219..221
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 225..227
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 229..233
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 236..241
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 249..261
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 272..277
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 286..290
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 296..298
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 315..317
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 320..324
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 331..342
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 346..351
FT /evidence="ECO:0007829|PDB:3H7C"
FT TURN 352..354
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 355..358
FT /evidence="ECO:0007829|PDB:3H7C"
FT TURN 359..361
FT /evidence="ECO:0007829|PDB:3H7C"
FT HELIX 364..367
FT /evidence="ECO:0007829|PDB:3H7C"
FT STRAND 368..372
FT /evidence="ECO:0007829|PDB:3H7C"
SQ SEQUENCE 383 AA; 43155 MW; E8289ED058B2BFD7 CRC64;
MEESRESPAE HGYYMPAEWD SHAQTWIGWP ERQDNWRHNA LPAQRVFADV AKAISKFEPV
TVCASPAQWE NARKQLPEDI RVVEMSMNDS WFRDSGPTFI VRKRPVKLSS LNRNIAGIDW
NFNAWGGAND GCYNDWSHDL LVSRKILALE RIPRFQHSMI LEGGSIHVDG EGTCLVTEEC
LLNKNRNPHM SKEQIEEELK KYLGVQSFIW LPRGLYGDED TNGHIDNMCC FARPGVVLLS
WTDDETDPQY ERSVEALSVL SNSIDARGRK IQVIKLYIPE PLYMTEEESS GITQDGEAIP
RLAGTRLAAS YVNFYIANGG IIAPQFGDPI RDKEAIRVLS DTFPHHSVVG IENAREIVLA
GGNIHCITQQ QPAEPTSVAE NGH
