EzCatDB: D00835
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DB codeD00835
CATH domainDomain 13.40.50.1970 : Rossmann fold
Domain 21.20.1090.10 : Dehydroquinate synthase-like, alpha domainCatalytic domain
E.C.1.1.1.6
MACiEM0312

CATH domainRelated DB codes (homologues)
1.20.1090.10 : Dehydroquinate synthase-like, alpha domainD00840
3.40.50.1970 : Rossmann foldD00840

Enzyme Name
UniProtKBKEGG

P32816Q97IL4Q9WYQ4O13702
Protein nameGlycerol dehydrogenase
Glycerol dehydrogenaseGlycerol dehydrogenaseGlycerol dehydrogenase
Glycerin dehydrogenase
NAD+-linked glycerol dehydrogenase
SynonymsGlyDH
GLDH
GDH
EC 1.1.1.6
Glycerol dehydrogenase
GLDH
GDH
EC 1.1.1.6
GLDH
GDH
EC 1.1.1.6
RefSeq
NP_348253.1 (Protein)
NC_003030.1 (DNA/RNA sequence)
NP_228233.1 (Protein)
NC_000853.1 (DNA/RNA sequence)
NP_593651.1 (Protein)
NM_001019083.2 (DNA/RNA sequence)
PfamPF00465 (Fe-ADH)
[Graphical view]

PF00465 (Fe-ADH)
[Graphical view]
PF00465 (Fe-ADH)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00561Glycerolipid metabolism

UniProtKB:Accession NumberP32816Q97IL4Q9WYQ4O13702
Entry nameGLDA_BACSTQ97IL4_CLOABGLDA_THEMAGLD1_SCHPO
ActivityGlycerol + NAD+ = glycerone + NADH.
Glycerol + NAD+ = glycerone + NADH.Glycerol + NAD+ = glycerone + NADH.
SubunitHomooctamer.


Subcellular location


Mitochondrion
CofactorBinds 1 zinc ion per subunit.
Binds 1 zinc ion per subunit (By similarity).Binds 1 zinc ion per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00038C00116C00003C00184C00004C00080
CompoundZincglycerolNAD+glyceroneNADHH+
Typeheavy metalcarbohydrateamide group,amine group,nucleotidecarbohydrateamide group,amine group,nucleotideothers
ChEBI29105
17754
15846
16016
16908
15378
PubChem32051
753
5893
670
439153
1038
              
1jpuA01UnboundUnboundUnboundUnboundUnbound 
1jq5A01UnboundUnboundBound:NADUnboundUnbound 
1jqaA01UnboundUnboundUnboundUnboundUnbound 
3ce9A01UnboundUnboundUnboundUnboundUnbound 
3ce9B01UnboundUnboundUnboundUnboundUnbound 
3ce9C01UnboundUnboundUnboundUnboundUnbound 
3ce9D01UnboundUnboundUnboundUnboundUnbound 
1ta9A01UnboundUnboundUnboundUnboundUnbound 
1ta9B01UnboundUnboundUnboundUnboundUnbound 
1kq3A01UnboundUnboundUnboundUnboundUnbound 
1jpuA02Bound:2x_ZNUnboundUnboundUnboundUnbound 
1jq5A02Bound:2x_ZNUnboundUnboundUnboundUnbound 
1jqaA02UnboundBound:GOLUnboundUnboundUnbound 
3ce9A02Bound:2x_ZNUnboundUnboundUnboundUnbound 
3ce9B02Bound:2x_ZNUnboundUnboundUnboundUnbound 
3ce9C02Bound:2x_ZNUnboundUnboundUnboundUnbound 
3ce9D02Bound:2x_ZNUnboundUnboundUnboundUnbound 
1ta9A02Bound:_Zn,Analogue;__KBound:GOL 1401UnboundUnboundUnbound 
1ta9B02Bound:_Zn,Analogue;__KBound:GOL 1402UnboundUnboundUnbound 
1kq3A02Bound:_Zn,Analogue;_CLAnalogue:TRSUnboundUnboundUnbound 

Active-site residues
resource
literature [3], [5], [6], [7], [9]
pdbCatalytic residuesCofactor-binding residuescomment
           
1jpuA01 
 
 
1jq5A01 
 
 
1jqaA01 
 
 
3ce9A01 
 
 
3ce9B01 
 
 
3ce9C01 
 
 
3ce9D01 
 
 
1ta9A01 
 
 
1ta9B01 
 
 
1kq3A01 
 
 
1jpuA02HIS 259
ASP 173;HIS 256;HIS 274(Catalytic zinc binding)
mutant S305C
1jq5A02HIS 259
ASP 173;HIS 256;HIS 274(Catalytic zinc binding)
mutant S305C
1jqaA02HIS 259
ASP 173;HIS 256;HIS 274(Catalytic zinc binding)
mutant S305C
3ce9A02HIS 254
ASP 171;HIS 250;HIS 266(Catalytic zinc binding)
 
3ce9B02HIS 254
ASP 171;HIS 250;HIS 266(Catalytic zinc binding)
 
3ce9C02HIS 254
ASP 171;HIS 250;HIS 266(Catalytic zinc binding)
 
3ce9D02HIS 254
ASP 171;HIS 250;HIS 266(Catalytic zinc binding)
 
1ta9A02HIS 318
ASP 232;HIS 315;HIS 333(Catalytic zinc binding)
 
1ta9B02HIS 318
ASP 232;HIS 315;HIS 333(Catalytic zinc binding)
 
1kq3A02HIS 255
ASP 169;HIS 252;HIS 269(Catalytic zinc binding)
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.790, p.795-796
[5]Fig.6, p.847
[6]p.371
[7]Fig.6, p.1080-1081
[9]p.3964-3966

references
[1]
PubMed ID8185833
JournalCrit Rev Microbiol
Year1994
Volume20
Pages13-56
AuthorsReid MF, Fewson CA
TitleMolecular characterization of microbial alcohol dehydrogenases.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 1-393 IN COMPLEX WITH NAD; ZINC AND SUBSTRATE ANALOG, SUBUNIT. F29
PubMed ID9685163
JournalNature
Year1998
Volume394
Pages299-302
AuthorsCarpenter EP, Hawkins AR, Frost JW, Brown KA
TitleStructure of dehydroquinate synthase reveals an active site capable of multistep catalysis.
Related PDB1dqs
Related UniProtKBP07547
[3]
CommentsX-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF MUTANT CYS-305 IN COMPLEXES WITH ZINC; NAD AND SUBSTRATE, DOMAIN, COFACTOR, SUBUNIT, MUTAGENESIS OF SER-305.
PubMed ID11566129
JournalStructure
Year2001
Volume9
Pages789-802
AuthorsRuzheinikov SN, Burke J, Sedelnikova S, Baker PJ, Taylor R, Bullough PA, Muir NM, Gore MG, Rice DW
TitleGlycerol dehydrogenase. structure, specificity, and mechanism of a family III polyol dehydrogenase.
Related PDB1jpu,1jq5,1jqa
Related UniProtKBP32816
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEX WITH ZINC AND SUBSTRATE ANALOG.
PubMed ID12193646
JournalProc Natl Acad Sci U S A
Year2002
Volume99
Pages11664-9
AuthorsLesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elsliger MA, Wooley J, Taylor SS, Hodgson KO, Wilson IA, Schultz PG, Stevens RC
TitleStructural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline.
Related PDB1kq3
Related UniProtKBQ9WYQ4
[5]
PubMed ID12909013
JournalJ Mol Biol
Year2003
Volume331
Pages829-60
AuthorsBartlett GJ, Borkakoti N, Thornton JM
TitleCatalysing new reactions during evolution: economy of residues and mechanism.
[6]
PubMed ID12486729
JournalProteins
Year2003
Volume50
Pages371-4
AuthorsBrinen LS, Canaves JM, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MA, Miller MD, Morse A, Moy K, Ouyang J, Robb A, Rodrigues K, Selby TL, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Taylor SS, Hodgson KO, Wooley J, Wilson IA
TitleCrystal structure of a zinc-containing glycerol dehydrogenase (TM0423) from Thermotoga maritima at 1.5 A resolution.
Related PDB1kq3
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
PubMed ID12962626
JournalStructure
Year2003
Volume11
Pages1071-85
AuthorsPauly TA, Ekstrom JL, Beebe DA, Chrunyk B, Cunningham D, Griffor M, Kamath A, Lee SE, Madura R, Mcguire D, Subashi T, Wasilko D, Watts P, Mylari BL, Oates PJ, Adams PD, Rath VL
TitleX-ray crystallographic and kinetic studies of human sorbitol dehydrogenase.
Related PDB1pl6,1pl7,1pl8
Related UniProtKBQ00796
[8]
PubMed ID15995211
JournalJ Bacteriol
Year2005
Volume187
Pages4957-66
AuthorsMontella C, Bellsolell L, Perez-Luque R, Badia J, Baldoma L, Coll M, Aguilar J
TitleCrystal structure of an iron-dependent group III dehydrogenase that interconverts L-lactaldehyde and L-1,2-propanediol in Escherichia coli.
Related PDB2bi4,2bl4
[9]
PubMed ID19011745
JournalCell Mol Life Sci
Year2008
Volume65
Pages3961-70
AuthorsAuld DS, Bergman T
TitleMedium- and short-chain dehydrogenase/reductase gene and protein families : The role of zinc for alcohol dehydrogenase structure and function.

comments
This enzyme belongs to the group III "iron-activated" alcohol dehydrogenases (literature [1] & [3]).
This enzyme is homologous to dehydroquinate synthase (EC=1.1.1.25; PDB 1dqs).
According to the literature [2] and [3], the hydride transfer reacion by this enzyme proceeds as follows:
(0) Zinc ion, which is bound to Asp173, His256 and His274 (PDB;1jpu) and interacts with two hydroxyl oxygens of substrate, glycerol, may lower the pKa of the C2 hydroxyl oxygen, facilitating its deprotonation.
(1) His259 might act as a general base to deprotonate the C2 hydroxyl oxygen, through a water molecule by proton shuttle, leading to an alkoxide transition-state.
(2) Hydride transfer from the C2 carbon atom to the C4 of the nicotinamide group in the NAD molecule occurs.

createdupdated
2010-02-042010-09-01


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Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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