P93031 (GMD2_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
GDP-mannose 4,6 dehydratase 2
EC=4.2.1.47

Alternative name(s):
GDP-D-mannose dehydratase 2
Short name=GMD 2

Gene names

Name:	MUR1
Synonyms:	GMD2
Ordered Locus Names:	At3g51160
ORF Names:	F24M12.200

Organism

Arabidopsis thaliana (Mouse-ear cress)

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	373 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Conversion of GDP-D-mannose to GDP-4-keto-6-D-deoxymannose. Ref.1
Catalytic activity	GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H2O.
Cofactor	NADP.
Pathway	Nucleotide-sugar biosynthesis; GDP-L-fucose biosynthesis via de novo pathway; GDP-L-fucose from GDP-alpha-D-mannose: step 1/2.
Subunit structure	Homotetramer. Binds to GER1. Ref.6
Sequence similarities	Belongs to the GDP-mannose 4,6-dehydratase family.

Ontologies

Keywords
Ligand	GTP-binding NADP Nucleotide-binding
Molecular function	Lyase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	'de novo' GDP-L-fucose biosynthetic process Inferred from mutant phenotype Ref.1. Source: TAIR GDP-mannose metabolic process Inferred from electronic annotation. Source: InterPro unidimensional cell growth Inferred from mutant phenotype. Source: TAIR
Cellular component	cytosol Inferred from direct assay. Source: TAIR
Molecular function	GDP-mannose 4,6-dehydratase activity Inferred from direct assay Ref.1. Source: TAIR GTP binding Inferred from electronic annotation. Source: UniProtKB-KW coenzyme binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 373

373

GDP-mannose 4,6 dehydratase 2

PRO_0000201711

Regions

Nucleotide binding

35 – 40

6

NADP

Nucleotide binding

91 – 92

2

NADP

Nucleotide binding

113 – 117

5

NADP

Region

220 – 228

9

Substrate binding

Region

314 – 317

4

Substrate binding

Sites

Active site

162

1

Active site

164

1

Nucleophile

Active site

185

1

Nucleophile

Binding site

60

1

NADP

Binding site

117

1

Substrate; via carbonyl oxygen

Binding site

128

1

NADP

Binding site

162

1

Substrate

Binding site

185

1

Substrate

Binding site

189

1

NADP

Binding site

214

1

Substrate

Binding site

215

1

NADP

Binding site

220

1

NADP

Binding site

247

1

Substrate; via amide nitrogen

Binding site

253

1

Substrate

Amino acid modifications

Modified residue

10

1

Phosphoserine Ref.7

Experimental info

Mutagenesis

107

1

P → L in mur1-2; strong reduction in L-fucose in the cell walls.

Mutagenesis

139

1

R → C in mur1-7; strong reduction in L-fucose in the cell walls.

Mutagenesis

153

1

R → C in mur1-5; strong reduction in L-fucose in the cell walls.

Mutagenesis

162

1

S → F in mur1-1; strong reduction in L-fucose in the cell walls.

Mutagenesis

191

1

A → V in mur1-3; strong reduction in L-fucose in the cell walls.

Mutagenesis

202

1

A → V in mur1-6; strong reduction in L-fucose in the cell walls.

Mutagenesis

210

1

G → Q in mur1-4; strong reduction in L-fucose in the cell walls.

Sequence conflict

55

1

V → F in AAM61140. Ref.5

Sequence conflict

179 – 181

3

FHP → IHL in CAB62638. Ref.2

Secondary structure

1

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373

Helix Strand Turn

Details...

Beta strand

30 – 34

5

Turn

35 – 37

3

Helix

39 – 49

11

Turn

50 – 52

3

Beta strand

54 – 59

6

Turn

68 – 73

6

Beta strand

84 – 89

6

Helix

95 – 105

11

Beta strand

108 – 112

5

Helix

119 – 124

6

Helix

126 – 133

8

Helix

135 – 151

17

Beta strand

156 – 162

7

Helix

163 – 166

4

Beta strand

171 – 173

3

Helix

184 – 203

20

Beta strand

206 – 212

7

Helix

225 – 237

13

Beta strand

244 – 247

4

Helix

258 – 268

11

Beta strand

271 – 273

3

Beta strand

276 – 279

4

Helix

287 – 297

11

Helix

302 – 304

3

Beta strand

306 – 308

3

Helix

310 – 312

3

Helix

326 – 332

7

Helix

340 – 362

23

Turn

363 – 365

3

Sequences

	Sequence		Length	Mass (Da)
	P93031 [UniParc]. Last modified November 22, 2005. Version 3. Checksum: 3AE1875B38BC1C82	FASTA	373	41,961
	10 20 30 40 50 60 MASENNGSRS DSESITAPKA DSTVVEPRKI ALITGITGQD GSYLTEFLLG KGYEVHGLIR 70 80 90 100 110 120 RSSNFNTQRI NHIYIDPHNV NKALMKLHYA DLTDASSLRR WIDVIKPDEV YNLAAQSHVA 130 140 150 160 170 180 VSFEIPDYTA DVVATGALRL LEAVRSHTID SGRTVKYYQA GSSEMFGSTP PPQSETTPFH 190 200 210 220 230 240 PRSPYAASKC AAHWYTVNYR EAYGLFACNG ILFNHESPRR GENFVTRKIT RALGRIKVGL 250 260 270 280 290 300 QTKLFLGNLQ ASRDWGFAGD YVEAMWLMLQ QEKPDDYVVA TEEGHTVEEF LDVSFGYLGL 310 320 330 340 350 360 NWKDYVEIDQ RYFRPAEVDN LQGDASKAKE VLGWKPQVGF EKLVKMMVDE DLELAKREKV 370 LVDAGYMDAK QQP

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The MUR1 gene of Arabidopsis thaliana encodes an isoform of GDP-D-mannose-4,6-dehydratase, catalyzing the first step in the de novo synthesis of GDP-L-fucose." Bonin C.P., Potter I., Vanzin G.F., Reiter W.-D. Proc. Natl. Acad. Sci. U.S.A. 94:2085-2090(1997) [PubMed: 9050909] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, MUTANTS MUR1-1; MUR1-2; MUR1-3; MUR1-4; MUR1-5; MUR1-9 AND MUR1-7. Strain: cv. Columbia.
[2]	"Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana." Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F. , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S. Nature 408:820-822(2000) [PubMed: 11130713] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"Arabidopsis ORF clones." Quinitio C., Chen H., Kim C.J., Shinn P., Ecker J.R. Submitted (JUN-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[5]	"Full-length cDNA from Arabidopsis thaliana." Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A. Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[6]	"Interaction of GDP-4-keto-6-deoxymannose-3,5-epimerase-4-reductase with GDP-mannose-4,6-dehydratase stabilizes the enzyme activity for formation of GDP-fucose from GDP-mannose." Nakayama K., Maeda Y., Jigami Y. Glycobiology 13:673-680(2003) [PubMed: 12881408] [Abstract] Cited for: INTERACTION WITH GER1.
[7]	"Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks." Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S. Plant Physiol. 150:889-903(2009) [PubMed: 19376835] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-10, MASS SPECTROMETRY. Strain: cv. Columbia. Tissue: Seedling.
[8]	"Structure of the MUR1 GDP-mannose 4,6-dehydratase from Arabidopsis thaliana: implications for ligand binding and specificity." Mulichak A.M., Bonin C.P., Reiter W.-D., Garavito R.M. Biochemistry 41:15578-15589(2002) [PubMed: 12501186] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 28-368 IN COMPLEX WITH NADP; GDP AND GDP-D-RHAMNOSE.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U81805 mRNA. Translation: AAB51505.1.
AL132980 Genomic DNA. Translation: CAB62638.1.
CP002686 Genomic DNA. Translation: AEE78758.1.
BT025710 mRNA. Translation: ABF82613.1.
AY084574 mRNA. Translation: AAM61140.1.

IPI

IPI00519785.

PIR

T45747.

RefSeq

NP_190685.2. NM_114976.3.

UniGene

At.23910.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1N7G	X-ray	2.20	A/B/C/D	1-373	[»]
1N7H	X-ray	1.80	A/B	1-373	[»]

ProteinModelPortal

P93031.

SMR

P93031. Positions 28-368.

ModBase

Search...

Protein-protein interaction databases

STRING

P93031.

Proteomic databases

PRIDE

P93031.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT3G51160.1; AT3G51160.1; AT3G51160.

GeneID

824280.

GenomeReviews

Gene locus AT3G51160 in contig BA000014_GR.

KEGG

ath:AT3G51160.

Organism-specific databases

GeneFarm

4170.

TAIR

At3g51160.

Phylogenomic databases

eggNOG

KOG1372.

HOGENOM

HBG755066.

InParanoid

P93031.

PhylomeDB

P93031.

ProtClustDB

PLN02653.

Enzyme and pathway databases

BioCyc

MetaCyc:AT3G51160-MONOMER.

Gene expression databases

ArrayExpress

P93031.

Genevestigator

P93031.

GermOnline

AT3G51160. Arabidopsis thaliana.

Family and domain databases

InterPro

IPR001509. Epimerase_deHydtase.
IPR006368. GDP_Man_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

Gene3D

G3DSA:3.40.50.720. NAD(P)-bd. 1 hit.

KO

K01711.

PANTHER

PTHR10366:SF32. GDP_mann_dehyd. 1 hit.

Pfam

PF01370. Epimerase. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01472. Gmd. 1 hit.

ProtoNet

Search...

Entry information

Entry name

GMD2_ARATH

Accession

Primary (citable) accession number: P93031
Secondary accession number(s): Q1ECM4, Q8LFY4, Q9SD30

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 16, 2004
Last sequence update:	November 22, 2005
Last modified:	November 16, 2011
This is version 88 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program