DB code: D00513

RLCP classification 9.1050.440000.8010 : Hydride transfer
8.131.164850.131 : Isomerization
5.14.411700.1 : Elimination
9.5010.536210.8010 : Hydride transfer
CATH domain 3.90.25.10 : UDP-galactose 4-epimerase; domain 1 Catalytic domain
3.40.50.720 : Rossmann fold Catalytic domain
E.C. 4.2.1.47
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.50.720 : Rossmann fold S00543 S00551 S00552 S00553 S00602 S00604 S00605 S00608 S00610 S00625 S00319 S00328 S00329 S00330 S00331 S00332 D00456 D00457 D00458 S00324 S00320 S00325 S00326 S00327 D00459 S00335 S00336 S00334 T00219 S00339 D00001 D00002 D00003 D00005 D00007 D00008 D00010 D00012 D00017 D00018 D00023 D00027 D00028 D00031 D00032 D00033 D00034 D00035 D00037 D00048 D00071 D00476 D00481 D00482 D00490 D00492 D00494 D00545 D00601 D00603 D00604 D00605 D00615 D00845 D00857 D00858 M00161 M00171 M00210 T00002 T00010 T00011 T00015 T00227 T00247 T00408 T00414 D00827 D00262 D00274 D00275 M00035 T00109
3.90.25.10 : UDP-galactose 4-epimerase; domain 1 D00601 D00604 D00262 D00274 D00275

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P93031 GDP-mannose 4,6 dehydratase 2
EC 4.2.1.47
GDP-D-mannose dehydratase 2
GMD 2
NP_190685.2 (Protein)
NM_114976.3 (DNA/RNA sequence)
PF01370 (Epimerase)
[Graphical View]

KEGG enzyme name
GDP-mannose 4,6-dehydratase
guanosine 5'-diphosphate-D-mannose oxidoreductase
guanosine diphosphomannose oxidoreductase
guanosine diphosphomannose 4,6-dehydratase
GDP-D-mannose dehydratase
GDP-D-mannose 4,6-dehydratase
Gmd
GDP-mannose 4,6-hydro-lyase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P93031 GMD2_ARATH GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H(2)O. Homotetramer. Binds to GER1. NADP.

KEGG Pathways
Map code Pathways E.C.
MAP00051 Fructose and mannose metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00006 C00096 C01222 C00001 I00088 I00089 I00090
E.C.
Compound NADP+ GDP-mannose GDP-4-dehydro-6-deoxy-D-mannose H2O GDP-4-dehydro-mannose GDP-4,5-ene-mannose GDP-6-deoxy-4-dehydro-5,6-ene-mannose
Type amide group,amine group,nucleotide amide group,amine group,carbohydrate,nucleotide amide group,amine group,carbohydrate,nucleotide H2O
ChEBI 18009
15820
16955
15377
PubChem 5886
18396
439446
22247451
962
1n7gA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:GDR Unbound Unbound Unbound
1n7gB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:GDR Unbound Unbound Unbound
1n7gC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:GDR Unbound Unbound Unbound
1n7gD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1n7hA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:GDP Unbound Unbound Unbound Unbound
1n7hB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:GDP Unbound Unbound Unbound Unbound
1n7gA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:NDP Unbound Unbound Unbound Unbound Unbound
1n7gB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:NDP Unbound Unbound Unbound Unbound Unbound
1n7gC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:NDP Unbound Unbound Unbound Unbound Unbound
1n7gD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:NDP Unbound Unbound Unbound Unbound Unbound
1n7hA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:NDP Unbound Unbound Unbound Unbound Unbound
1n7hB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:NDP Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [1], [4], [5]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1n7gA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 253
1n7gB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 253
1n7gC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 253
1n7gD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 253
1n7hA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 253
1n7hB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 253
1n7gA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 162;GLU 164;TYR 185;LYS 189
1n7gB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 162;GLU 164;TYR 185;LYS 189
1n7gC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 162;GLU 164;TYR 185;LYS 189
1n7gD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 162;GLU 164;TYR 185;LYS 189
1n7hA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 162;GLU 164;TYR 185;LYS 189
1n7hB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 162;GLU 164;TYR 185;LYS 189

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.8, p.131-132 3
[4]
Fig.1, p.15586 3
[5]
Fig.4, p.533-535

References
[1]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID 20139699
PubMed ID 10673432
Journal Structure Fold Des
Year 2000
Volume 8
Pages 123-35
Authors Somoza JR, Menon S, Schmidt H, Joseph-McCarthy D, Dessen A, Stahl ML, Somers WS, Sullivan FX
Title Structural and kinetic analysis of Escherichia coli GDP-mannose 4,6 dehydratase provides insights into the enzyme's catalytic mechanism and regulation by GDP-fucose.
Related PDB 1db3
Related UniProtKB P0AC88
[2]
Resource
Comments
Medline ID
PubMed ID 11444851
Journal Biochem Biophys Res Commun
Year 2001
Volume 285
Pages 364-71
Authors Wu B, Zhang Y, Wang PG
Title Identification and characterization of GDP-d-mannose 4,6-dehydratase and GDP-l-fucose snthetase in a GDP-l-fucose biosynthetic gene cluster from Helicobacter pylori.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 11096116
Journal J Biol Chem
Year 2001
Volume 276
Pages 5577-83
Authors Kneidinger B, Graninger M, Adam G, Puchberger M, Kosma P, Zayni S, Messner P
Title Identification of two GDP-6-deoxy-D-lyxo-4-hexulose reductases synthesizing GDP-D-rhamnose in Aneurinibacillus thermoaerophilus L420-91T.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 12501186
Journal Biochemistry
Year 2002
Volume 41
Pages 15578-89
Authors Mulichak AM, Bonin CP, Reiter WD, Garavito RM
Title Structure of the MUR1 GDP-mannose 4,6-dehydratase from Arabidopsis thaliana: implications for ligand binding and specificity.
Related PDB 1n7g 1n7h
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 14739333
Journal Protein Sci
Year 2004
Volume 13
Pages 529-39
Authors Webb NA, Mulichak AM, Lam JS, Rocchetta HL, Garavito RM
Title Crystal structure of a tetrameric GDP-D-mannose 4,6-dehydratase from a bacterial GDP-D-rhamnose biosynthetic pathway.
Related PDB 1rpn
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 15493979
Journal Biochem Soc Trans
Year 2004
Volume 32
Pages 647-54
Authors Naismith JH
Title Chemical insights from structural studies of enzymes.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the Short-chain dehydrogenases/reductases (SDR).
Although a catalytic residue is different, this enzyme is homologous to the counterpart enzyme from bacteria and human (D00543 in EzCatDB).
This enzyme catalyzes reactions similar to those by its homologous enzyme, dTDP-D-glucose-4,6-dehydratase (EC 4.2.1.46, D00262 in EzCatDB) (see [5] and [6]). The difference from the homologous enzyme is that this enzyme has only one acidic residue as a general acid/base, whearas the homologue uses two acidic residues.
According to the literature [4], [5] and [6], this enzyme catalyzes at least three reactions: oxidation of GDP-mannose (hydride transfer from GDP-mannose to nicotinamide), dehydration (elimination of a hydroxyl group from C6), and rereduction of C5-C6 double bond to methyl group (hydride transfer from nicotinamide to the intermediate).
Taken together, this enzyme catalyzes the following reactions:
(A) Hydride transfer from C4 atom of substrate to NADP, forming a 4-keto intermediate (I00088):
(A0) Lys189 (of 1n7g) modulates the activity (or pKa) of Tyr185 via 2'-hydroxyl group of NADP, along with the N1 atom of the nicotinamide group in NADP, whereas Ser162 modulates the pKa of 4-hydroxyl oxygen of the substrate.
(A1) Tyr185 acts as a general base to deprotonate the 4-hydroxyl oxygen of the substrate. Meanwhile, the hydride transfer occurs from the C4-carbon of the substrate to the C4 atom of the nicotinamide, forming 4-keto intermediate.
(B) Isomerization from the 4-keto intermediato to form an enol/enolate intermediate (I00089):
(B0) Arg253 might modulate the pKa of Glu164 as a general base. Moreover, the 4-keto carbonyl group may increase the acidity of the C5 atom.
(B1) Glu164 acts as a general base to deprotonate the C5 atom, leading to formation of enol/enolate intermediate.
(C) Elimination of hydroxyl group from C6 of the enol/enolate intermediate, forming 4-keto-5,6-mannosen intermediate (I00090):
(C0) GDP-phosphoryl groups in the intermediate might modulate the pKa of Glu164 as a general acid.
(C1) Glu164 acts as a general acid to protonate O6 hydroxyl group, to release a water molecule, and to form the 4-keto-5,6-ene intermediate from the enol/enolate intermediate.
(D) Hydride transfer from NAD(P)H to C6 atom of the intermediate:
(D0) A slight rotation of the hexose ring of intermediate might be necessary for the reaction. Lys189 modulates the activity (or pKa) of Tyr185 via 2'-hydroxyl group of NADP, along with the N1 atom of the nicotinamide group in NADP.
(D1) Hydride transfer from NAD(P)H to C6 atom of the hexose ring in the intermediate. Meanwhile, a general acid must protonate the C5 atom of the hexose. According to the literature [5], Ser162, which is corresponding to Thr126 (of 1rpn in D00543), seems to be positioned to play a role as a general acid. Since this residue is close enough to Tyr185, Tyr185 might act as a general acid via Thr126 to protonate the C5 atom.

Created Updated
2004-06-28 2011-12-26