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
CATH 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

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 18009	15820 15820	16955 16955	15377 15377
PubChem	5886 5886	18396 18396	439446 439446	22247451 962 22247451 962

1n7gA01	Unbound	Unbound	Analogue:GDR		Unbound	Unbound	Unbound
1n7gB01	Unbound	Unbound	Analogue:GDR		Unbound	Unbound	Unbound
1n7gC01	Unbound	Unbound	Analogue:GDR		Unbound	Unbound	Unbound
1n7gD01	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound
1n7hA01	Unbound	Analogue:GDP	Unbound		Unbound	Unbound	Unbound
1n7hB01	Unbound	Analogue:GDP	Unbound		Unbound	Unbound	Unbound
1n7gA02	Bound:NDP	Unbound	Unbound		Unbound	Unbound	Unbound
1n7gB02	Bound:NDP	Unbound	Unbound		Unbound	Unbound	Unbound
1n7gC02	Bound:NDP	Unbound	Unbound		Unbound	Unbound	Unbound
1n7gD02	Bound:NDP	Unbound	Unbound		Unbound	Unbound	Unbound
1n7hA02	Bound:NDP	Unbound	Unbound		Unbound	Unbound	Unbound
1n7hB02	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	ARG 253
1n7gB01	ARG 253
1n7gC01	ARG 253
1n7gD01	ARG 253
1n7hA01	ARG 253
1n7hB01	ARG 253
1n7gA02	SER 162;GLU 164;TYR 185;LYS 189
1n7gB02	SER 162;GLU 164;TYR 185;LYS 189
1n7gC02	SER 162;GLU 164;TYR 185;LYS 189
1n7gD02	SER 162;GLU 164;TYR 185;LYS 189
1n7hA02	SER 162;GLU 164;TYR 185;LYS 189
1n7hB02	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.

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