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
CATH 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	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 15846	18009 18009	15820 15820	16955 16955	15377 15377
PubChem	5893 5893	5886 5886	18396 18396	439446 439446	22247451 962 22247451 962

1db3A01	Unbound	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound
1rpnA01	Unbound	Bound:NDP	Unbound	Unbound		Unbound	Unbound	Unbound
1rpnB01	Unbound	Bound:NDP	Unbound	Unbound		Unbound	Unbound	Unbound
1rpnC01	Unbound	Bound:NDP	Unbound	Unbound		Unbound	Unbound	Unbound
1rpnD01	Unbound	Bound:NDP	Unbound	Unbound		Unbound	Unbound	Unbound
1t2aA01	Unbound	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound
1t2aB01	Unbound	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound
1t2aC01	Unbound	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound
1t2aD01	Unbound	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound
1db3A02	Unbound	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound
1rpnA02	Unbound	Unbound	Analogue:GDP	Unbound		Unbound	Unbound	Unbound
1rpnB02	Unbound	Unbound	Analogue:GDP	Unbound		Unbound	Unbound	Unbound
1rpnC02	Unbound	Unbound	Analogue:GDP	Unbound		Unbound	Unbound	Unbound
1rpnD02	Unbound	Unbound	Analogue:GDP	Unbound		Unbound	Unbound	Unbound
1t2aA02	Unbound	Unbound	Analogue:GDP	Unbound		Unbound	Unbound	Unbound
1t2aB02	Unbound	Unbound	Analogue:GDP	Unbound		Unbound	Unbound	Unbound
1t2aC02	Unbound	Unbound	Analogue:GDP	Unbound		Unbound	Unbound	Unbound
1t2aD02	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	THR 132;GLU 134;TYR 156;LYS 160
1rpnA01	THR 126;GLU 128;TYR 150;LYS 154
1rpnB01	THR 126;GLU 128;TYR 150;LYS 154
1rpnC01	THR 126;GLU 128;TYR 150;LYS 154
1rpnD01	THR 126;GLU 128;TYR 150;LYS 154
1t2aA01	THR 155;GLU 157;TYR 179;LYS 183
1t2aB01	THR 155;GLU 157;TYR 179;LYS 183
1t2aC01	THR 155;GLU 157;TYR 179;LYS 183
1t2aD01	THR 155;GLU 157;TYR 179;LYS 183
1db3A02	ARG 224
1rpnA02	ARG 218
1rpnB02	ARG 218
1rpnC02	ARG 218
1rpnD02	ARG 218
1t2aA02	ARG 247
1t2aB02	ARG 247
1t2aC02	ARG 247
1t2aD02	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.

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