GMD2_ARATH
ID GMD2_ARATH Reviewed; 373 AA.
AC P93031; Q1ECM4; Q8LFY4; Q9SD30;
DT 16-AUG-2004, integrated into UniProtKB/Swiss-Prot.
DT 22-NOV-2005, sequence version 3.
DT 03-AUG-2022, entry version 149.
DE RecName: Full=GDP-mannose 4,6 dehydratase 2;
DE EC=4.2.1.47;
DE AltName: Full=GDP-D-mannose dehydratase 2;
DE Short=GMD 2;
GN Name=MUR1; Synonyms=GMD2; OrderedLocusNames=At3g51160; ORFNames=F24M12.200;
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 [MRNA], FUNCTION, CATALYTIC ACTIVITY, AND MUTANTS
RP MUR1-1; MUR1-2; MUR1-3; MUR1-4; MUR1-5; MUR1-9 AND MUR1-7.
RC STRAIN=cv. Columbia;
RX PubMed=9050909; DOI=10.1073/pnas.94.5.2085;
RA Bonin C.P., Potter I., Vanzin G.F., Reiter W.-D.;
RT "The MUR1 gene of Arabidopsis thaliana encodes an isoform of GDP-D-mannose-
RT 4,6-dehydratase, catalyzing the first step in the de novo synthesis of GDP-
RT L-fucose.";
RL Proc. Natl. Acad. Sci. U.S.A. 94:2085-2090(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Quinitio C., Chen H., Kim C.J., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (JUN-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP INTERACTION WITH GER1.
RX PubMed=12881408; DOI=10.1093/glycob/cwg099;
RA Nakayama K., Maeda Y., Jigami Y.;
RT "Interaction of GDP-4-keto-6-deoxymannose-3,5-epimerase-4-reductase with
RT GDP-mannose-4,6-dehydratase stabilizes the enzyme activity for formation of
RT GDP-fucose from GDP-mannose.";
RL Glycobiology 13:673-680(2003).
RN [7]
RP FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=12805618; DOI=10.1104/pp.103.022368;
RA Bonin C.P., Freshour G., Hahn M.G., Vanzin G.F., Reiter W.D.;
RT "The GMD1 and GMD2 genes of Arabidopsis encode isoforms of GDP-D-mannose
RT 4,6-dehydratase with cell type-specific expression patterns.";
RL Plant Physiol. 132:883-892(2003).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Root;
RX PubMed=18433157; DOI=10.1021/pr8000173;
RA de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E.,
RA Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C., Lorkovic Z.J.,
RA Barta A., Lecourieux D., Verhounig A., Jonak C., Hirt H.;
RT "Site-specific phosphorylation profiling of Arabidopsis proteins by mass
RT spectrometry and peptide chip analysis.";
RL J. Proteome Res. 7:2458-2470(2008).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 28-368 IN COMPLEX WITH NADP; GDP
RP AND GDP-D-RHAMNOSE, AND ACTIVE SITE.
RX PubMed=12501186; DOI=10.1021/bi0266683;
RA Mulichak A.M., Bonin C.P., Reiter W.-D., Garavito R.M.;
RT "Structure of the MUR1 GDP-mannose 4,6-dehydratase from Arabidopsis
RT thaliana: implications for ligand binding and specificity.";
RL Biochemistry 41:15578-15589(2002).
CC -!- FUNCTION: Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-
CC deoxy-D-mannose. {ECO:0000269|PubMed:12805618,
CC ECO:0000269|PubMed:9050909}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H2O;
CC Xref=Rhea:RHEA:23820, ChEBI:CHEBI:15377, ChEBI:CHEBI:57527,
CC ChEBI:CHEBI:57964; EC=4.2.1.47;
CC Evidence={ECO:0000269|PubMed:9050909};
CC -!- COFACTOR:
CC Name=NADP(+); Xref=ChEBI:CHEBI:58349;
CC -!- PATHWAY: Nucleotide-sugar biosynthesis; GDP-L-fucose biosynthesis via
CC de novo pathway; GDP-L-fucose from GDP-alpha-D-mannose: step 1/2.
CC -!- SUBUNIT: Homotetramer. Binds to GER1. {ECO:0000269|PubMed:12501186}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, flowers, siliques, leaves and
CC stems. Not expressed in the root meristem and the proximal part of the
CC elongation zone, or in emerging lateral roots. Expressed in trichomes
CC and guard cells, and in pollen just before anthesis.
CC {ECO:0000269|PubMed:12805618}.
CC -!- SIMILARITY: Belongs to the NAD(P)-dependent epimerase/dehydratase
CC family. GDP-mannose 4,6-dehydratase subfamily. {ECO:0000305}.
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DR EMBL; U81805; AAB51505.1; -; mRNA.
DR EMBL; AL132980; CAB62638.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78758.1; -; Genomic_DNA.
DR EMBL; BT025710; ABF82613.1; -; mRNA.
DR EMBL; AY084574; AAM61140.1; -; mRNA.
DR PIR; T45747; T45747.
DR RefSeq; NP_190685.2; NM_114976.4.
DR PDB; 1N7G; X-ray; 2.20 A; A/B/C/D=1-373.
DR PDB; 1N7H; X-ray; 1.80 A; A/B=1-373.
DR PDBsum; 1N7G; -.
DR PDBsum; 1N7H; -.
DR AlphaFoldDB; P93031; -.
DR SMR; P93031; -.
DR BioGRID; 9598; 4.
DR STRING; 3702.AT3G51160.1; -.
DR iPTMnet; P93031; -.
DR MetOSite; P93031; -.
DR PaxDb; P93031; -.
DR PRIDE; P93031; -.
DR ProteomicsDB; 247371; -.
DR EnsemblPlants; AT3G51160.1; AT3G51160.1; AT3G51160.
DR GeneID; 824280; -.
DR Gramene; AT3G51160.1; AT3G51160.1; AT3G51160.
DR KEGG; ath:AT3G51160; -.
DR Araport; AT3G51160; -.
DR TAIR; locus:2080933; AT3G51160.
DR eggNOG; KOG1372; Eukaryota.
DR HOGENOM; CLU_007383_14_0_1; -.
DR InParanoid; P93031; -.
DR OMA; FVKSSWQ; -.
DR OrthoDB; 877551at2759; -.
DR PhylomeDB; P93031; -.
DR BioCyc; ARA:AT3G51160-MON; -.
DR BioCyc; MetaCyc:AT3G51160-MON; -.
DR BRENDA; 4.2.1.47; 399.
DR UniPathway; UPA00128; UER00190.
DR EvolutionaryTrace; P93031; -.
DR PRO; PR:P93031; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; P93031; baseline and differential.
DR Genevisible; P93031; AT.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0008446; F:GDP-mannose 4,6-dehydratase activity; IDA:TAIR.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0042351; P:'de novo' GDP-L-fucose biosynthetic process; IMP:TAIR.
DR GO; GO:0019673; P:GDP-mannose metabolic process; IBA:GO_Central.
DR GO; GO:0009826; P:unidimensional cell growth; IMP:TAIR.
DR HAMAP; MF_00955; GDP_Man_dehydratase; 1.
DR InterPro; IPR006368; GDP_Man_deHydtase.
DR InterPro; IPR016040; NAD(P)-bd_dom.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR PANTHER; PTHR43715; PTHR43715; 1.
DR Pfam; PF16363; GDP_Man_Dehyd; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR01472; gmd; 1.
PE 1: Evidence at protein level;
KW 3D-structure; GTP-binding; Lyase; NADP; Nucleotide-binding;
KW Reference proteome.
FT CHAIN 1..373
FT /note="GDP-mannose 4,6 dehydratase 2"
FT /id="PRO_0000201711"
FT REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..19
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 162
FT /evidence="ECO:0000305|PubMed:12501186"
FT ACT_SITE 164
FT /note="Nucleophile"
FT /evidence="ECO:0000305|PubMed:12501186"
FT ACT_SITE 185
FT /note="Nucleophile"
FT /evidence="ECO:0000305|PubMed:12501186"
FT BINDING 35..40
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:12501186"
FT BINDING 60
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:12501186"
FT BINDING 91..92
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:12501186"
FT BINDING 113..117
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:12501186"
FT BINDING 117
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12501186"
FT BINDING 128
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:12501186"
FT BINDING 162
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12501186"
FT BINDING 185
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12501186"
FT BINDING 189
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:12501186"
FT BINDING 214
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12501186"
FT BINDING 215
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:12501186"
FT BINDING 220..228
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12501186"
FT BINDING 220
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:12501186"
FT BINDING 247
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12501186"
FT BINDING 253
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12501186"
FT BINDING 314..317
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12501186"
FT MUTAGEN 107
FT /note="P->L: In mur1-2; strong reduction in L-fucose in the
FT cell walls."
FT /evidence="ECO:0000269|PubMed:9050909"
FT MUTAGEN 139
FT /note="R->C: In mur1-7; strong reduction in L-fucose in the
FT cell walls."
FT /evidence="ECO:0000269|PubMed:9050909"
FT MUTAGEN 153
FT /note="R->C: In mur1-5; strong reduction in L-fucose in the
FT cell walls."
FT /evidence="ECO:0000269|PubMed:9050909"
FT MUTAGEN 162
FT /note="S->F: In mur1-1; strong reduction in L-fucose in the
FT cell walls."
FT /evidence="ECO:0000269|PubMed:9050909"
FT MUTAGEN 191
FT /note="A->V: In mur1-3; strong reduction in L-fucose in the
FT cell walls."
FT /evidence="ECO:0000269|PubMed:9050909"
FT MUTAGEN 202
FT /note="A->V: In mur1-6; strong reduction in L-fucose in the
FT cell walls."
FT /evidence="ECO:0000269|PubMed:9050909"
FT MUTAGEN 210
FT /note="G->Q: In mur1-4; strong reduction in L-fucose in the
FT cell walls."
FT /evidence="ECO:0000269|PubMed:9050909"
FT CONFLICT 55
FT /note="V -> F (in Ref. 5; AAM61140)"
FT /evidence="ECO:0000305"
FT CONFLICT 179..181
FT /note="FHP -> IHL (in Ref. 2; CAB62638)"
FT /evidence="ECO:0000305"
FT STRAND 30..34
FT /evidence="ECO:0007829|PDB:1N7H"
FT TURN 35..37
FT /evidence="ECO:0007829|PDB:1N7H"
FT HELIX 39..50
FT /evidence="ECO:0007829|PDB:1N7H"
FT STRAND 54..59
FT /evidence="ECO:0007829|PDB:1N7H"
FT TURN 68..73
FT /evidence="ECO:0007829|PDB:1N7H"
FT STRAND 85..89
FT /evidence="ECO:0007829|PDB:1N7H"
FT HELIX 95..105
FT /evidence="ECO:0007829|PDB:1N7H"
FT STRAND 108..112
FT /evidence="ECO:0007829|PDB:1N7H"
FT HELIX 119..124
FT /evidence="ECO:0007829|PDB:1N7H"
FT HELIX 126..133
FT /evidence="ECO:0007829|PDB:1N7H"
FT HELIX 135..151
FT /evidence="ECO:0007829|PDB:1N7H"
FT STRAND 156..162
FT /evidence="ECO:0007829|PDB:1N7H"
FT HELIX 163..166
FT /evidence="ECO:0007829|PDB:1N7H"
FT STRAND 171..173
FT /evidence="ECO:0007829|PDB:1N7H"
FT HELIX 184..203
FT /evidence="ECO:0007829|PDB:1N7H"
FT STRAND 206..212
FT /evidence="ECO:0007829|PDB:1N7H"
FT HELIX 225..237
FT /evidence="ECO:0007829|PDB:1N7H"
FT STRAND 244..247
FT /evidence="ECO:0007829|PDB:1N7H"
FT STRAND 252..254
FT /evidence="ECO:0007829|PDB:1N7H"
FT HELIX 258..269
FT /evidence="ECO:0007829|PDB:1N7H"
FT STRAND 271..273
FT /evidence="ECO:0007829|PDB:1N7H"
FT STRAND 276..279
FT /evidence="ECO:0007829|PDB:1N7H"
FT STRAND 284..286
FT /evidence="ECO:0007829|PDB:1N7H"
FT HELIX 287..297
FT /evidence="ECO:0007829|PDB:1N7H"
FT HELIX 302..304
FT /evidence="ECO:0007829|PDB:1N7H"
FT STRAND 306..308
FT /evidence="ECO:0007829|PDB:1N7H"
FT HELIX 310..312
FT /evidence="ECO:0007829|PDB:1N7H"
FT HELIX 326..332
FT /evidence="ECO:0007829|PDB:1N7H"
FT HELIX 340..363
FT /evidence="ECO:0007829|PDB:1N7H"
SQ SEQUENCE 373 AA; 41961 MW; 3AE1875B38BC1C82 CRC64;
MASENNGSRS DSESITAPKA DSTVVEPRKI ALITGITGQD GSYLTEFLLG KGYEVHGLIR
RSSNFNTQRI NHIYIDPHNV NKALMKLHYA DLTDASSLRR WIDVIKPDEV YNLAAQSHVA
VSFEIPDYTA DVVATGALRL LEAVRSHTID SGRTVKYYQA GSSEMFGSTP PPQSETTPFH
PRSPYAASKC AAHWYTVNYR EAYGLFACNG ILFNHESPRR GENFVTRKIT RALGRIKVGL
QTKLFLGNLQ ASRDWGFAGD YVEAMWLMLQ QEKPDDYVVA TEEGHTVEEF LDVSFGYLGL
NWKDYVEIDQ RYFRPAEVDN LQGDASKAKE VLGWKPQVGF EKLVKMMVDE DLELAKREKV
LVDAGYMDAK QQP
