DB code: D00543

RLCP classification 9.1050.440000.8011 : Hydride transfer
8.131.164850.131 : Isomerization
5.14.411700.1 : Elimination
9.5010.536210.8011 : Hydride transfer
CATH domain 3.40.50.720 : Rossmann fold Catalytic domain
3.90.25.10 : UDP-galactose 4-epimerase; domain 1 Catalytic domain
E.C. 4.2.1.47
CSA 1db3
M-CSA 1db3
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0AC88 GDP-mannose 4,6-dehydratase
EC 4.2.1.47
GDP-D-mannose dehydratase
NP_416557.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490295.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01370 (Epimerase)
[Graphical View]
Q51366 GDP-mannose 4,6-dehydratase
EC 4.2.1.47
GDP-D-mannose dehydratase
NP_254140.1 (Protein)
NC_002516.2 (DNA/RNA sequence)
PF01370 (Epimerase)
[Graphical View]
O60547 GDP-mannose 4,6 dehydratase
EC 4.2.1.47
GDP-D-mannose dehydratase
GMD
NP_001240775.1 (Protein)
NM_001253846.1 (DNA/RNA sequence)
NP_001491.1 (Protein)
NM_001500.3 (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
P0AC88 GM4D_ECOLI GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H(2)O. Homodimer. NADP.
Q51366 GM4D_PSEAE GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H(2)O. NAD.
O60547 GMDS_HUMAN GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H(2)O. NADP.

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

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00003 C00006 C00096 C01222 C00001 I00088 I00089 I00090
E.C.
Compound NAD+ 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,nucleotide amide group,amine group,carbohydrate,nucleotide amide group,amine group,carbohydrate,nucleotide H2O
ChEBI 15846
18009
15820
16955
15377
PubChem 5893
5886
18396
439446
22247451
962
1db3A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1rpnA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NDP Unbound Unbound Unbound Unbound Unbound
1rpnB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NDP Unbound Unbound Unbound Unbound Unbound
1rpnC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NDP Unbound Unbound Unbound Unbound Unbound
1rpnD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NDP Unbound Unbound Unbound Unbound Unbound
1t2aA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1t2aB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1t2aC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1t2aD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1db3A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1rpnA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:GDP Unbound Unbound Unbound Unbound
1rpnB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:GDP Unbound Unbound Unbound Unbound
1rpnC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:GDP Unbound Unbound Unbound Unbound
1rpnD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:GDP Unbound Unbound Unbound Unbound
1t2aA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:GDP Unbound Unbound Unbound Unbound
1t2aB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:GDP Unbound Unbound Unbound Unbound
1t2aC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:GDP Unbound Unbound Unbound Unbound
1t2aD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:GDP 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
1db3A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 132;GLU 134;TYR 156;LYS 160
1rpnA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 126;GLU 128;TYR 150;LYS 154
1rpnB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 126;GLU 128;TYR 150;LYS 154
1rpnC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 126;GLU 128;TYR 150;LYS 154
1rpnD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 126;GLU 128;TYR 150;LYS 154
1t2aA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 155;GLU 157;TYR 179;LYS 183
1t2aB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 155;GLU 157;TYR 179;LYS 183
1t2aC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 155;GLU 157;TYR 179;LYS 183
1t2aD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 155;GLU 157;TYR 179;LYS 183
1db3A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 224
1rpnA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 218
1rpnB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 218
1rpnC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 218
1rpnD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 218
1t2aA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 247
1t2aB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 247
1t2aC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 247
1t2aD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 247

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 Arabidopsis (D00513 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 NAD(P), forming a 4-keto intermediate (I00088):
(A0) Lys154 (of 1rpn) modulates the activity (or pKa) of Tyr150 via 2'-hydroxyl group of NAD(P), along with the N1 atom of the nicotinamide group in NAD(P), whereas Thr126 modulates the pKa of 4-hydroxyl oxygen of the substrate.
(A1) Tyr150 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) Arg218 might modulate the pKa of Glu128 as a general base. Moreover, the 4-keto carbonyl group may increase the acidity of the C5 atom.
(B1) Glu128 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 Glu128 as a general acid.
(C1) Glu128 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. Lys154 modulates the activity (or pKa) of Tyr150 via 2'-hydroxyl group of NAD(P), along with the N1 atom of the nicotinamide group in NAD(P).
(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], Thr126 seems to be positioned to play a role as a general acid. Since this residue is close enough to Tyr150, Tyr150 might act as a general acid via Thr126 to protonate the C5 atom.

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