EzCatDB: D00275

DB codeD00275
RLCP classification9.1050.440000.8010
9.5010.536200.8010
CATH domainDomain 13.40.50.720Catalytic domain
Domain 23.90.25.10Catalytic domain
E.C.5.1.3.20
CSA1eq2

CATH domainRelated DB codes (homologues)
3.40.50.720S00543,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,T00408,T00414,D00827,D00262,D00274,M00035,T00109
3.90.25.10D00513,D00601,D00604,D00262,D00274

Enzyme Name
Swiss-protKEGG

P67910
Protein nameADP-L-glycero-D-manno-heptose-6-epimeraseADP-glyceromanno-heptose 6-epimerase
SynonymsEC 5.1.3.20
ADP-L-glycero-beta-D-manno-heptose-6-epimerase
ADP-glyceromanno-heptose 6-epimerase
ADP-hep 6-epimerase
AGME

KEGG pathways
MAP codePathways
MAP00540Lipopolysaccharide biosynthesis

Swiss-prot:Accession NumberP67910
Entry nameHLDD_ECOLI
ActivityADP-D-glycero-D-manno-heptose = ADP-L-glycero- D-manno-heptose.
SubunitHomopentamer.
Subcellular location
CofactorBinds 1 NADP(+) per subunit. NAD(+) can substitute for NADP(+), but enzymatic activity is reduced.


CofactorsSubstratesProductsintermediates
KEGG-idC00006C06397C06398I00096
CompoundNADP+ADP-D-glycero-D-manno-heptoseADP-L-glycero-D-manno-heptoseADP-D-glycero-D-manno-6-keto-heptose
Typeamide group,amine group,nucleotideamine group,carbohydrate,nucleotideamine group,carbohydrate,nucleotide
1eq2A01Bound:NAPUnboundUnbound
1eq2B01Bound:NAPUnboundUnbound
1eq2C01Bound:NAPUnboundUnbound
1eq2D01Bound:NAPUnboundUnbound
1eq2E01Bound:NAPUnboundUnbound
1eq2F01Bound:NAPUnboundUnbound
1eq2G01Bound:NAPUnboundUnbound
1eq2H01Bound:NAPUnboundUnbound
1eq2I01Bound:NAPUnboundUnbound
1eq2J01Bound:NAPUnboundUnbound
2x6tA01Bound:NAPUnboundUnbound
2x6tB01Bound:NAPUnboundUnbound
2x6tC01Bound:NAPUnboundUnbound
2x6tD01Bound:NAPUnboundUnbound
2x6tE01Bound:NAPUnboundUnbound
2x6tF01Bound:NAPUnboundUnbound
2x6tG01Bound:NAPUnboundUnbound
2x6tH01Bound:NAPUnboundUnbound
2x6tI01Bound:NAPUnboundUnbound
2x6tJ01Bound:NAPUnboundUnbound
2x86A01Bound:NAPUnboundUnbound
2x86B01Bound:NAPUnboundUnbound
2x86C01Bound:NAPUnboundUnbound
2x86D01Bound:NAPUnboundUnbound
2x86E01Bound:NAPUnboundUnbound
2x86F01Bound:NAPUnboundUnbound
2x86G01Bound:NAPUnboundUnbound
2x86H01Bound:NAPUnboundUnbound
2x86I01Bound:NAPUnboundUnbound
2x86J01Bound:NAPUnboundUnbound
2x86K01Bound:NAPUnboundUnbound
2x86L01Bound:NAPUnboundUnbound
2x86M01Bound:NAPUnboundUnbound
2x86N01Bound:NAPUnboundUnbound
2x86O01Bound:NAPUnboundUnbound
2x86P01Bound:NAPUnboundUnbound
2x86Q01Bound:NAPUnboundUnbound
2x86R01Bound:NAPUnboundUnbound
2x86S01Bound:NAPUnboundUnbound
2x86T01Bound:NAPUnboundUnbound
1eq2A02UnboundUnboundAnalogue:ADQ
1eq2B02UnboundAnalogue:ADQUnbound
1eq2C02UnboundUnboundAnalogue:ADQ
1eq2D02UnboundAnalogue:ADQUnbound
1eq2E02UnboundUnboundAnalogue:ADQ
1eq2F02UnboundAnalogue:ADQUnbound
1eq2G02UnboundUnboundAnalogue:ADQ
1eq2H02UnboundUnboundAnalogue:ADQ
1eq2I02UnboundUnboundAnalogue:ADQ
1eq2J02UnboundUnboundAnalogue:ADQ
2x6tA02UnboundAnalogue:ADP-BMAUnbound
2x6tB02UnboundAnalogue:ADP-BMAUnbound
2x6tC02UnboundAnalogue:ADP-BMAUnbound
2x6tD02UnboundAnalogue:ADP-BMAUnbound
2x6tE02UnboundAnalogue:ADP-BMAUnbound
2x6tF02UnboundAnalogue:ADP-BMAUnbound
2x6tG02UnboundAnalogue:ADP-BMAUnbound
2x6tH02UnboundAnalogue:ADP-BMAUnbound
2x6tI02UnboundAnalogue:ADP-BMAUnbound
2x6tJ02UnboundAnalogue:ADP-BMAUnbound
2x86A02UnboundUnboundAnalogue:ADP-BMA
2x86B02UnboundAnalogue:ADPUnbound
2x86C02UnboundAnalogue:ADP-BMAUnbound
2x86D02UnboundUnboundAnalogue:ADP-BMA
2x86E02UnboundUnboundAnalogue:ADP-BMA
2x86F02UnboundAnalogue:ADP-BMAUnbound
2x86G02UnboundAnalogue:ADP-BMAUnbound
2x86H02UnboundUnboundAnalogue:ADP-BMA
2x86I02UnboundAnalogue:ADP-BMAUnbound
2x86J02UnboundUnboundAnalogue:ADP-BMA
2x86K02UnboundUnboundAnalogue:ADP-BMA
2x86L02UnboundUnboundAnalogue:ADP-BMA
2x86M02UnboundAnalogue:ADP-BMAUnbound
2x86N02UnboundUnboundAnalogue:ADP-BMA
2x86O02UnboundUnboundAnalogue:ADP-BMA
2x86P02UnboundUnboundAnalogue:ADP-BMA
2x86Q02UnboundUnboundAnalogue:ADP-BMA
2x86R02UnboundAnalogue:ADP-BMAUnbound
2x86S02UnboundUnboundAnalogue:ADP-BMA
2x86T02UnboundUnboundAnalogue:ADP-BMA

Active-site residues
resource
PDB;1eq2 & Swiss-prot;P67910 & literature [3], [6], [8]
pdbCatalytic residuesModified residuescomment
1eq2A01SER 116;TYR 140;LYS 144
CSO 78(S-Hydroxy-cysteine)

1eq2B01SER 116;TYR 140;LYS 144
CSO 78(S-Hydroxy-cysteine)

1eq2C01SER 116;TYR 140;LYS 144
CSO 78(S-Hydroxy-cysteine)

1eq2D01SER 116;TYR 140;LYS 144
CSO 78(S-Hydroxy-cysteine)

1eq2E01SER 116;TYR 140;LYS 144
CSO 78(S-Hydroxy-cysteine)

1eq2F01SER 116;TYR 140;LYS 144
CSO 78(S-Hydroxy-cysteine)

1eq2G01SER 116;TYR 140;LYS 144
CSO 78(S-Hydroxy-cysteine)

1eq2H01SER 116;TYR 140;LYS 144
CSO 78(S-Hydroxy-cysteine)

1eq2I01SER 116;TYR 140;LYS 144
CSO 78(S-Hydroxy-cysteine)

1eq2J01SER 116;TYR 140;LYS 144
CSO 78(S-Hydroxy-cysteine)

2x6tA01SER 116;       ;LYS 144

mutant Y140F
2x6tB01SER 116;       ;LYS 144

mutant Y140F
2x6tC01SER 116;       ;LYS 144

mutant Y140F
2x6tD01SER 116;       ;LYS 144

mutant Y140F
2x6tE01SER 116;       ;LYS 144

mutant Y140F
2x6tF01SER 116;       ;LYS 144

mutant Y140F
2x6tG01SER 116;       ;LYS 144

mutant Y140F
2x6tH01SER 116;       ;LYS 144

mutant Y140F
2x6tI01SER 116;       ;LYS 144

mutant Y140F
2x6tJ01SER 116;       ;LYS 144

mutant Y140F
2x86A01SER 116;       ;LYS 144

mutant Y140F
2x86B01SER 116;       ;LYS 144

mutant Y140F
2x86C01SER 116;       ;LYS 144

mutant Y140F
2x86D01SER 116;       ;LYS 144

mutant Y140F
2x86E01SER 116;       ;LYS 144

mutant Y140F
2x86F01SER 116;       ;LYS 144

mutant Y140F
2x86G01SER 116;       ;LYS 144

mutant Y140F
2x86H01SER 116;       ;LYS 144

mutant Y140F
2x86I01SER 116;       ;LYS 144

mutant Y140F
2x86J01SER 116;       ;LYS 144

mutant Y140F
2x86K01SER 116;       ;LYS 144

mutant Y140F
2x86L01SER 116;       ;LYS 144

mutant Y140F
2x86M01SER 116;       ;LYS 144

mutant Y140F
2x86N01SER 116;       ;LYS 144

mutant Y140F
2x86O01SER 116;       ;LYS 144

mutant Y140F
2x86P01SER 116;       ;LYS 144

mutant Y140F
2x86Q01SER 116;       ;LYS 144

mutant Y140F
2x86R01SER 116;       ;LYS 144

mutant Y140F
2x86S01SER 116;       ;LYS 144

mutant Y140F
2x86T01SER 116;       ;LYS 144

mutant Y140F
1eq2A02LYS 178

invisible 195-207,251-271
1eq2B02LYS 178

invisible 265-271
1eq2C02LYS 178

invisible 194-206,250-271
1eq2D02LYS 178


1eq2E02LYS 178

invisible 265-271
1eq2F02LYS 178


1eq2G02LYS 178


1eq2H02LYS 178

invisible 262-271
1eq2I02LYS 178


1eq2J02LYS 178

invisible 265-271
2x6tA02LYS 178


2x6tB02LYS 178


2x6tC02LYS 178


2x6tD02LYS 178


2x6tE02LYS 178


2x6tF02LYS 178


2x6tG02LYS 178


2x6tH02LYS 178


2x6tI02LYS 178


2x6tJ02LYS 178


2x86A02LYS 178


2x86B02LYS 178


2x86C02LYS 178


2x86D02LYS 178


2x86E02LYS 178


2x86F02LYS 178


2x86G02LYS 178


2x86H02LYS 178


2x86I02LYS 178


2x86J02LYS 178


2x86K02LYS 178


2x86L02LYS 178


2x86M02LYS 178


2x86N02LYS 178


2x86O02LYS 178


2x86P02LYS 178


2x86Q02LYS 178


2x86R02LYS 178


2x86S02LYS 178


2x86T02LYS 178



References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.460
[4]Fig.3, Fig.4, p.1655-16563
[7]Scheme 1, p.8878-8879
[8]FIGURE 7, p.5914
[10]Fig.3, Fig.6, p.3922-3923
[11]Fig.3, p.1340-1341

references
[1]
CommentsCHARACTERIZATION.
Medline ID95014184
PubMed ID7929099
JournalJ Biol Chem
Year1994
Volume269
Pages24384-90
AuthorsDing L, Seto BL, Ahmed SA, Coleman WG Jr
TitlePurification and properties of the Escherichia coli K-12 NAD-dependent nucleotide diphosphosugar epimerase, ADP-L-glycero-D-mannoheptose 6-epimerase.
Related Swiss-protP67910
[2]
CommentsCRYSTALLIZATION.
PubMed ID10089470
JournalActa Crystallogr D Biol Crystallogr
Year1999
Volume55
Pages685-8
AuthorsDing L, Zhang Y, Deacon AM, Ealick SE, Ni Y, Sun P, Coleman WG Jr
TitleCrystallization and preliminary X-ray diffraction studies of the lipopolysaccharide core biosynthetic enzyme ADP-L-glycero-D-mannoheptose 6-epimerase from Escherichia coli K-12.
Related Swiss-protP67910
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF COMPLEX WITH NADP AND ADP-GLUCOSE, AND SUBUNIT.
PubMed ID10896473
JournalStructure Fold Des
Year2000
Volume8
Pages453-62
AuthorsDeacon AM, Ni YS, Coleman WG Jr, Ealick SE
TitleThe crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase: catalysis with a twist.
Related PDB1eq2
Related Swiss-protP67910
[4]
PubMed ID11706991
JournalCell Mol Life Sci
Year2001
Volume58
Pages1650-65
AuthorsAllard ST, Giraud MF, Naismith JH
TitleEpimerases: structure, function and mechanism.
[5]
CommentsCOFACTOR.
PubMed ID11313358
JournalJ Biol Chem
Year2001
Volume276
Pages27329-34
AuthorsNi Y, McPhie P, Deacon A, Ealick S, Coleman WG Jr
TitleEvidence that NADP+ is the physiological cofactor of ADP-L-glycero-D-mannoheptose 6-epimerase.
Related Swiss-protP67910
[6]
PubMed ID12137277
JournalNat Prod Rep
Year2002
Volume19
Pages261-77
AuthorsSamuel J, Tanner ME
TitleMechanistic aspects of enzymatic carbohydrate epimerization.
[7]
PubMed ID15264802
JournalJ Am Chem Soc
Year2004
Volume126
Pages8878-9
AuthorsRead JA, Ahmed RA, Morrison JP, Coleman WG Jr, Tanner ME
TitleThe mechanism of the reaction catalyzed by ADP-beta-L-glycero-D-manno-heptose 6-epimerase.
[8]
PubMed ID15823050
JournalBiochemistry
Year2005
Volume44
Pages5907-15
AuthorsMorrison JP, Read JA, Coleman WG Jr, Tanner ME
TitleDismutase activity of ADP-L-glycero-D-manno-heptose 6-epimerase: evidence for a direct oxidation/reduction mechanism.
[9]
PubMed ID15932222
JournalOrg Lett
Year2005
Volume7
Pages2457-60
AuthorsRead JA, Ahmed RA, Tanner ME
TitleEfficient chemoenzymatic synthesis of ADP-D-glycero-beta-D-manno-heptose and a mechanistic study of ADP-L-glycero-D-manno-heptose 6-epimerase.
[10]
PubMed ID17316025
JournalBiochemistry
Year2007
Volume46
Pages3916-24
AuthorsMorrison JP, Tanner ME
TitleA two-base mechanism for Escherichia coli ADP-L-glycero-D-manno-heptose 6-epimerase.
[11]
PubMed ID20506248
JournalProtein Sci
Year2010
Volume19
Pages1337-43
AuthorsKowatz T, Morrison JP, Tanner ME, Naismith JH
TitleThe crystal structure of the Y140F mutant of ADP-L-glycero-D-manno-heptose 6-epimerase bound to ADP-beta-D-mannose suggests a one base mechanism.
Related PDB2x6t,2x86

comments
This enzyme is homologous to UDP-glucose 4-epimerase (E.C. 5.1.3.2, D00274 in EzCatDB).
This enzyme is a distant homologue of the short-chain dehydrogenase/reductase (SDR) superfamily, which includes Drosophia alcohol dehydrogenase (S00319 in EzCatDB). This enzyme has got a catalytic triad composed of conserved residues, Ser, Tyr, and Lys. The conformation of these residues, compared to that of the NAD molecule, seems to be similar to that of the homologous enzymes.
According to the literature [4], [7] & [8], this enzyme catalyzes the following reactions:
(A) Hydride transfer from C6" atom of the substrate to NADP(+), forming a ketone intermediate and NADPH:
(X) Rotation of the reactive part around the C5"-C6" bond in the intermediate:
(B) Hydride transfer from NADPH to the ketone intermediate:
Here, between the two hydride transfer reactions, a conformational change of the intermediate would occur to expose the opposite face of carbonyl to the cofactor.
Moreover, according to the literature [8], [10] and [11], there are two possible mechanisms, a two base mechanism and a one base mechanism.
In the two base mechanism (see [8] and [10]), two distinct sets of general base might be involved in the two hydride transfer reactions. In the (A) reaction, Tyr140 from the catalytic triad might act as a general base, whereas Lys178 might act as a general acid in the (B) reaction (see [10]).
In the one base mechanism, Tyr140 from the catalytic triad seems to act as a general base in the (A) reaction, and as a general acid in the (B) reaction. In this mechanism, Tyr140 adjusts its position in response to the rotation of the intermediate (see [11]).
Considering the active site of this enzyme (2x6t and 2x86), the one base mechanism is more likely, as Lys178 is too far away from the reactive site. Lys178 is involved in binding of the substrate/intermediate, rather than in catalysis.

createdupdated
2004-04-052011-07-07


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
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)

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