DB code: T00408

RLCP classification 9.1050.439980.119 : Hydride transfer
4.501.3944060.57 : Addition
9.1050.584160.119 : Hydride transfer
1.14.800.129 : Hydrolysis
CATH domain 3.40.50.720 : Rossmann fold Catalytic domain
1.-.-.- : Catalytic domain
3.40.50.720 : Rossmann fold Catalytic domain
E.C. 1.1.1.132
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 D00513 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 T00414 D00827 D00262 D00274 D00275 M00035 T00109

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P11759 GDP-mannose 6-dehydrogenase
GMD
EC 1.1.1.132
NP_252230.1 (Protein)
NC_002516.2 (DNA/RNA sequence)
PF00984 (UDPG_MGDP_dh)
PF03720 (UDPG_MGDP_dh_C)
PF03721 (UDPG_MGDP_dh_N)
[Graphical View]

KEGG enzyme name
GDP-mannose 6-dehydrogenase
Guanosine diphosphomannose dehydrogenase
GDP-mannose dehydrogenase
Guanosine diphosphomannose dehydrogenase
Guanosine diphospho-D-mannose dehydrogenase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P11759 ALGD_PSEAE GDP-D-mannose + 2 NAD(+) + H(2)O = GDP-D-mannuronate + 2 NADH. Homotetramer (Potential). According to Ref.6, this enzyme exists as a homotetramer, but results obtained in Ref.3 and Ref.5 indicate that it is a homohexamer.

KEGG Pathways
Map code Pathways E.C.
MAP00051 Fructose and mannose metabolism
MAP00520 Amino sugar and nucleotide sugar metabolism

Compound table
Substrates Products Intermediates
KEGG-id C00096 C00003 C00001 C00976 C00004 C00080 I00103 I00104 I00105
E.C.
Compound GDP-D-mannose NAD+ H2O GDP-D-mannuronate NADH H+ GDP-6-dehydro-D-mannose Protein [GDP-6-S-D-mannose]-L-cysteine Protein [GDP-6-S-6-dehydro-D-mannose]-L-cysteine
Type amide group,amine group,carbohydrate,nucleotide amide group,amine group,nucleotide H2O amide group,amine group,carbohydrate,carboxyl group,nucleotide amide group,amine group,nucleotide others
ChEBI 15820
15846
15377
85507
16908
15378
PubChem 18396
5893
22247451
962
447152
439153
1038
1mfzA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1mfzB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1mfzC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1mfzD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1muuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:NAD Unbound Unbound
1muuB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:NAD Unbound Unbound
1muuC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:NAD Unbound Unbound
1muuD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:NAD Unbound Unbound
1mv8A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:NAD Unbound Unbound
1mv8B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:NAD Unbound Unbound
1mv8C01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:NAD Unbound Unbound
1mv8D01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:NAD Unbound Unbound
1mfzA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1mfzB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1mfzC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1mfzD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1muuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1muuB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1muuC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1muuD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1mv8A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1mv8B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1mv8C02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1mv8D02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1mfzA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:GDX Unbound
1mfzB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:GDX Unbound
1mfzC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:GDX Unbound
1mfzD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:GDX Unbound
1muuA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:GDX Unbound
1muuB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:GDX Unbound
1muuC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:GDX Unbound
1muuD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:GDX Unbound
1mv8A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:GDX Unbound
1mv8B03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:GDX Unbound
1mv8C03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:GDX Unbound
1mv8D03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:GDX 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
1mfzA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 124;GLU 157
1mfzB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 124;GLU 157
1mfzC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 124;GLU 157
1mfzD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 124;GLU 157
1muuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 124;GLU 157
1muuB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 124;GLU 157
1muuC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 124;GLU 157
1muuD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 124;GLU 157
1mv8A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 124;GLU 157
1mv8B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 124;GLU 157
1mv8C01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 124;GLU 157
1mv8D01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain THR 124;GLU 157
1mfzA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 210;ASN 214
1mfzB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 210;ASN 214
1mfzC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 210;ASN 214
1mfzD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 210;ASN 214
1muuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 210;ASN 214
1muuB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 210;ASN 214
1muuC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 210;ASN 214
1muuD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 210;ASN 214
1mv8A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 210;ASN 214
1mv8B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 210;ASN 214
1mv8C02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 210;ASN 214
1mv8D02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 210;ASN 214
1mfzA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 268;LYS 271;ASP 272
1mfzB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 268;LYS 271;ASP 272
1mfzC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 268;LYS 271;ASP 272
1mfzD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 268;LYS 271;ASP 272
1muuA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 268;LYS 271;ASP 272
1muuB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 268;LYS 271;ASP 272
1muuC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 268;LYS 271;ASP 272
1muuD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 268;LYS 271;ASP 272
1mv8A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 268;LYS 271;ASP 272
1mv8B03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 268;LYS 271;ASP 272
1mv8C03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 268;LYS 271;ASP 272
1mv8D03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 268;LYS 271;ASP 272

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.9384-9385
[4]
Fig.1, p.4666-4667
[5]
p.138-139

References
[1]
Resource
Comments
Medline ID
PubMed ID 2470755
Journal J Biol Chem
Year 1989
Volume 264
Pages 9380-5
Authors Roychoudhury S, May TB, Gill JF, Singh SK, Feingold DS, Chakrabarty AM
Title Purification and characterization of guanosine diphospho-D-mannose dehydrogenase. A key enzyme in the biosynthesis of alginate by Pseudomonas aeruginosa.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 8638483
Journal Adv Enzymol Relat Areas Mol Biol
Year 1995
Volume 70
Pages 221-55
Authors Shankar S, Ye RW, Schlictman D, Chakrabarty AM
Title Exopolysaccharide alginate synthesis in Pseudomonas aeruginosa: enzymology and regulation of gene expression.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.31 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND NAD, MUTAGENESIS OF CYS-260.
Medline ID
PubMed ID 10841783
Journal Biochemistry
Year 2000
Volume 39
Pages 7012-23
Authors Campbell RE, Mosimann SC, van De Rijn I, Tanner ME, Strynadka NC
Title The first structure of UDP-glucose dehydrogenase reveals the catalytic residues necessary for the two-fold oxidation.
Related PDB 1dli 1dlj
Related UniProtKB P0C0F4
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEX WITH NAD AND PRODUCT.
Medline ID
PubMed ID 12705829
Journal Biochemistry
Year 2003
Volume 42
Pages 4658-68
Authors Snook CF, Tipton PA, Beamer LJ
Title Crystal structure of GDP-mannose dehydrogenase: a key enzyme of alginate biosynthesis in P. aeruginosa.
Related PDB 1mfz 1muu 1mv8
Related UniProtKB P11759
[5]
Resource
Comments
Medline ID
PubMed ID 16111644
Journal Arch Biochem Biophys
Year 2005
Volume 441
Pages 132-40
Authors Kimmel JL, Tipton PA
Title Inactivation of GDP-mannose dehydrogenase from Pseudomonas aeruginosa by penicillic acid identifies a critical active site loop.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the small group of NAD+-dependent four-electron-transfer dehydrogenases (literature [5]).
This enzyme is homologous to UDP-glucose 6-dehydrogenase (EC=1.1.1.22, T00227 in EzCatDB), although their second domains are classified into different categories in the structural classification (CATH).
According to the literature [3] and [4], this enzyme catalyzes the following reactions:
(A) Hydride transfer from C6' atom of GDP-mannose to nicotinamide of NAD, forming an aldehyde intermediate, GDP-6-dehydro-D-mannose (I00103):
(A1) Lys210 acts as a general base to deprotonate the hydroxyl oxygen, whereas hydride transfer occurs from C6' atom to nicotinamide of NAD. (Here, instead of Lys210, Asp272' (from the adjacent chain) may act as a general base to deprotonate the C6' atom through a water, with Thr124 interacting with C6' through the same water molecule. Thr124 may modulate the pKa of C6' atom through the water, and Asn214 may modulate the pKa of Asp272'.)
(B) Addition of Cys268 to carbonyl C6' atom of the aldehyde intermediate, forming the second thiohemiacetal intermediate (I00104):
(B0) Lys271' (from adjacent chain) and (a positive charged dipole of) a nearby alpha-helix modulates and lowers the pKa of Cys268' to activate the nucleophilic residue.
(B1) The activated Cys268' makes a nucleophilic attack on the aldehyde intermediate.
(B2) Lys210 and Asp272'/Thr124 may stabilize the oxyanion produced by the addition reaction.
(C) Hydride transfer from C6' atom of the thiohemiacetal intermediate to nicotinamide of NAD, forming the third thioester intermediate (I00105):
(C0) Lys210 and Asp272'/Thr124 may stabilize the oxyanion of the intermediate. (Asp272' and Thr124 interact with the oxyanion through a water.)
(C1) Collapse of the oxyanion leads to the hydride transfer from C6' atom to nicotinamide of NAD, forming the thioester intermediate.
(D) Hydrolysis of the thioester intermediate:
(D1) Glu157 acts as a general base to deprotonate and activate a water molecule.
(D2) The activated water makes a nucleophilic attack on the thioester group, leading to an oxyanion transition-state. The oxyanion is stabilized by Lys210 and Asp272'/Thr124. (Asp272' and Thr124 interact with the oxyanion through a water.)
(D3) The oxyanion collapses and Cys268 is released.

Created Updated
2010-09-02 2011-09-13