DB code: D00275

RLCP classification 9.1050.440000.8010 : Hydride transfer
9.5010.536200.8010 : Hydride transfer
CATH domain 3.40.50.720 : Rossmann fold Catalytic domain
3.90.25.10 : UDP-galactose 4-epimerase; domain 1 Catalytic domain
E.C. 5.1.3.20
CSA 1eq2
M-CSA 1eq2
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 T00408 T00414 D00827 D00262 D00274 M00035 T00109
3.90.25.10 : UDP-galactose 4-epimerase; domain 1 D00513 D00601 D00604 D00262 D00274

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P67910 ADP-L-glycero-D-manno-heptose-6-epimerase
EC 5.1.3.20
ADP-L-glycero-beta-D-manno-heptose-6-epimerase
ADP-glyceromanno-heptose 6-epimerase
ADP-hep 6-epimerase
AGME
NP_418076.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491814.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01370 (Epimerase)
[Graphical View]

KEGG enzyme name
ADP-glyceromanno-heptose 6-epimerase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P67910 HLDD_ECOLI ADP-D-glycero-D-manno-heptose = ADP-L-glycero- D-manno-heptose. Homopentamer. Binds 1 NADP(+) per subunit. NAD(+) can substitute for NADP(+), but enzymatic activity is reduced.

KEGG Pathways
Map code Pathways E.C.
MAP00540 Lipopolysaccharide biosynthesis

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00006 C06397 C06398 I00096
E.C.
Compound NADP+ ADP-D-glycero-D-manno-heptose ADP-L-glycero-D-manno-heptose ADP-D-glycero-D-manno-6-keto-heptose
Type amide group,amine group,nucleotide amine group,carbohydrate,nucleotide amine group,carbohydrate,nucleotide
ChEBI 18009
 18009
 		59966
 59966
 		61530
 61530
PubChem 5886
 5886
 		23724494
 46173178
 23724494
 46173178
 		11444938
 46173345
 11444938
 46173345
1eq2A01 Bound:NAP Unbound Unbound
1eq2B01 Bound:NAP Unbound Unbound
1eq2C01 Bound:NAP Unbound Unbound
1eq2D01 Bound:NAP Unbound Unbound
1eq2E01 Bound:NAP Unbound Unbound
1eq2F01 Bound:NAP Unbound Unbound
1eq2G01 Bound:NAP Unbound Unbound
1eq2H01 Bound:NAP Unbound Unbound
1eq2I01 Bound:NAP Unbound Unbound
1eq2J01 Bound:NAP Unbound Unbound
2x6tA01 Bound:NAP Unbound Unbound
2x6tB01 Bound:NAP Unbound Unbound
2x6tC01 Bound:NAP Unbound Unbound
2x6tD01 Bound:NAP Unbound Unbound
2x6tE01 Bound:NAP Unbound Unbound
2x6tF01 Bound:NAP Unbound Unbound
2x6tG01 Bound:NAP Unbound Unbound
2x6tH01 Bound:NAP Unbound Unbound
2x6tI01 Bound:NAP Unbound Unbound
2x6tJ01 Bound:NAP Unbound Unbound
2x86A01 Bound:NAP Unbound Unbound
2x86B01 Bound:NAP Unbound Unbound
2x86C01 Bound:NAP Unbound Unbound
2x86D01 Bound:NAP Unbound Unbound
2x86E01 Bound:NAP Unbound Unbound
2x86F01 Bound:NAP Unbound Unbound
2x86G01 Bound:NAP Unbound Unbound
2x86H01 Bound:NAP Unbound Unbound
2x86I01 Bound:NAP Unbound Unbound
2x86J01 Bound:NAP Unbound Unbound
2x86K01 Bound:NAP Unbound Unbound
2x86L01 Bound:NAP Unbound Unbound
2x86M01 Bound:NAP Unbound Unbound
2x86N01 Bound:NAP Unbound Unbound
2x86O01 Bound:NAP Unbound Unbound
2x86P01 Bound:NAP Unbound Unbound
2x86Q01 Bound:NAP Unbound Unbound
2x86R01 Bound:NAP Unbound Unbound
2x86S01 Bound:NAP Unbound Unbound
2x86T01 Bound:NAP Unbound Unbound
1eq2A02 Unbound Unbound Analogue:ADQ
1eq2B02 Unbound Analogue:ADQ Unbound
1eq2C02 Unbound Unbound Analogue:ADQ
1eq2D02 Unbound Analogue:ADQ Unbound
1eq2E02 Unbound Unbound Analogue:ADQ
1eq2F02 Unbound Analogue:ADQ Unbound
1eq2G02 Unbound Unbound Analogue:ADQ
1eq2H02 Unbound Unbound Analogue:ADQ
1eq2I02 Unbound Unbound Analogue:ADQ
1eq2J02 Unbound Unbound Analogue:ADQ
2x6tA02 Unbound Analogue:ADP-BMA Unbound
2x6tB02 Unbound Analogue:ADP-BMA Unbound
2x6tC02 Unbound Analogue:ADP-BMA Unbound
2x6tD02 Unbound Analogue:ADP-BMA Unbound
2x6tE02 Unbound Analogue:ADP-BMA Unbound
2x6tF02 Unbound Analogue:ADP-BMA Unbound
2x6tG02 Unbound Analogue:ADP-BMA Unbound
2x6tH02 Unbound Analogue:ADP-BMA Unbound
2x6tI02 Unbound Analogue:ADP-BMA Unbound
2x6tJ02 Unbound Analogue:ADP-BMA Unbound
2x86A02 Unbound Unbound Analogue:ADP-BMA
2x86B02 Unbound Analogue:ADP Unbound
2x86C02 Unbound Analogue:ADP-BMA Unbound
2x86D02 Unbound Unbound Analogue:ADP-BMA
2x86E02 Unbound Unbound Analogue:ADP-BMA
2x86F02 Unbound Analogue:ADP-BMA Unbound
2x86G02 Unbound Analogue:ADP-BMA Unbound
2x86H02 Unbound Unbound Analogue:ADP-BMA
2x86I02 Unbound Analogue:ADP-BMA Unbound
2x86J02 Unbound Unbound Analogue:ADP-BMA
2x86K02 Unbound Unbound Analogue:ADP-BMA
2x86L02 Unbound Unbound Analogue:ADP-BMA
2x86M02 Unbound Analogue:ADP-BMA Unbound
2x86N02 Unbound Unbound Analogue:ADP-BMA
2x86O02 Unbound Unbound Analogue:ADP-BMA
2x86P02 Unbound Unbound Analogue:ADP-BMA
2x86Q02 Unbound Unbound Analogue:ADP-BMA
2x86R02 Unbound Analogue:ADP-BMA Unbound
2x86S02 Unbound Unbound Analogue:ADP-BMA
2x86T02 Unbound Unbound Analogue:ADP-BMA

Reference for Active-site residues
resource references E.C.
PDB;1eq2 & Swiss-prot;P67910 & literature [3], [6], [8]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1eq2A01 SER 116;TYR 140;LYS 144 CSO 78(S-Hydroxy-cysteine)
1eq2B01 SER 116;TYR 140;LYS 144 CSO 78(S-Hydroxy-cysteine)
1eq2C01 SER 116;TYR 140;LYS 144 CSO 78(S-Hydroxy-cysteine)
1eq2D01 SER 116;TYR 140;LYS 144 CSO 78(S-Hydroxy-cysteine)
1eq2E01 SER 116;TYR 140;LYS 144 CSO 78(S-Hydroxy-cysteine)
1eq2F01 SER 116;TYR 140;LYS 144 CSO 78(S-Hydroxy-cysteine)
1eq2G01 SER 116;TYR 140;LYS 144 CSO 78(S-Hydroxy-cysteine)
1eq2H01 SER 116;TYR 140;LYS 144 CSO 78(S-Hydroxy-cysteine)
1eq2I01 SER 116;TYR 140;LYS 144 CSO 78(S-Hydroxy-cysteine)
1eq2J01 SER 116;TYR 140;LYS 144 CSO 78(S-Hydroxy-cysteine)
2x6tA01 SER 116;;LYS 144 mutant Y140F
2x6tB01 SER 116;;LYS 144 mutant Y140F
2x6tC01 SER 116;;LYS 144 mutant Y140F
2x6tD01 SER 116;;LYS 144 mutant Y140F
2x6tE01 SER 116;;LYS 144 mutant Y140F
2x6tF01 SER 116;;LYS 144 mutant Y140F
2x6tG01 SER 116;;LYS 144 mutant Y140F
2x6tH01 SER 116;;LYS 144 mutant Y140F
2x6tI01 SER 116;;LYS 144 mutant Y140F
2x6tJ01 SER 116;;LYS 144 mutant Y140F
2x86A01 SER 116;;LYS 144 mutant Y140F
2x86B01 SER 116;;LYS 144 mutant Y140F
2x86C01 SER 116;;LYS 144 mutant Y140F
2x86D01 SER 116;;LYS 144 mutant Y140F
2x86E01 SER 116;;LYS 144 mutant Y140F
2x86F01 SER 116;;LYS 144 mutant Y140F
2x86G01 SER 116;;LYS 144 mutant Y140F
2x86H01 SER 116;;LYS 144 mutant Y140F
2x86I01 SER 116;;LYS 144 mutant Y140F
2x86J01 SER 116;;LYS 144 mutant Y140F
2x86K01 SER 116;;LYS 144 mutant Y140F
2x86L01 SER 116;;LYS 144 mutant Y140F
2x86M01 SER 116;;LYS 144 mutant Y140F
2x86N01 SER 116;;LYS 144 mutant Y140F
2x86O01 SER 116;;LYS 144 mutant Y140F
2x86P01 SER 116;;LYS 144 mutant Y140F
2x86Q01 SER 116;;LYS 144 mutant Y140F
2x86R01 SER 116;;LYS 144 mutant Y140F
2x86S01 SER 116;;LYS 144 mutant Y140F
2x86T01 SER 116;;LYS 144 mutant Y140F
1eq2A02 LYS 178 invisible 195-207,251-271
1eq2B02 LYS 178 invisible 265-271
1eq2C02 LYS 178 invisible 194-206,250-271
1eq2D02 LYS 178
1eq2E02 LYS 178 invisible 265-271
1eq2F02 LYS 178
1eq2G02 LYS 178
1eq2H02 LYS 178 invisible 262-271
1eq2I02 LYS 178
1eq2J02 LYS 178 invisible 265-271
2x6tA02 LYS 178
2x6tB02 LYS 178
2x6tC02 LYS 178
2x6tD02 LYS 178
2x6tE02 LYS 178
2x6tF02 LYS 178
2x6tG02 LYS 178
2x6tH02 LYS 178
2x6tI02 LYS 178
2x6tJ02 LYS 178
2x86A02 LYS 178
2x86B02 LYS 178
2x86C02 LYS 178
2x86D02 LYS 178
2x86E02 LYS 178
2x86F02 LYS 178
2x86G02 LYS 178
2x86H02 LYS 178
2x86I02 LYS 178
2x86J02 LYS 178
2x86K02 LYS 178
2x86L02 LYS 178
2x86M02 LYS 178
2x86N02 LYS 178
2x86O02 LYS 178
2x86P02 LYS 178
2x86Q02 LYS 178
2x86R02 LYS 178
2x86S02 LYS 178
2x86T02 LYS 178

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
p.460
[4]
Fig.3, Fig.4, p.1655-1656 3
[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]
Resource
Comments CHARACTERIZATION.
Medline ID 95014184
PubMed ID 7929099
Journal J Biol Chem
Year 1994
Volume 269
Pages 24384-90
Authors Ding L, Seto BL, Ahmed SA, Coleman WG Jr
Title Purification and properties of the Escherichia coli K-12 NAD-dependent nucleotide diphosphosugar epimerase, ADP-L-glycero-D-mannoheptose 6-epimerase.
Related PDB
Related UniProtKB P67910
[2]
Resource
Comments CRYSTALLIZATION.
Medline ID
PubMed ID 10089470
Journal Acta Crystallogr D Biol Crystallogr
Year 1999
Volume 55
Pages 685-8
Authors Ding L, Zhang Y, Deacon AM, Ealick SE, Ni Y, Sun P, Coleman WG Jr
Title Crystallization 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 PDB
Related UniProtKB P67910
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF COMPLEX WITH NADP AND ADP-GLUCOSE, AND SUBUNIT.
Medline ID
PubMed ID 10896473
Journal Structure Fold Des
Year 2000
Volume 8
Pages 453-62
Authors Deacon AM, Ni YS, Coleman WG Jr, Ealick SE
Title The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase: catalysis with a twist.
Related PDB 1eq2
Related UniProtKB P67910
[4]
Resource
Comments
Medline ID
PubMed ID 11706991
Journal Cell Mol Life Sci
Year 2001
Volume 58
Pages 1650-65
Authors Allard ST, Giraud MF, Naismith JH
Title Epimerases: structure, function and mechanism.
Related PDB
Related UniProtKB
[5]
Resource
Comments COFACTOR.
Medline ID
PubMed ID 11313358
Journal J Biol Chem
Year 2001
Volume 276
Pages 27329-34
Authors Ni Y, McPhie P, Deacon A, Ealick S, Coleman WG Jr
Title Evidence that NADP+ is the physiological cofactor of ADP-L-glycero-D-mannoheptose 6-epimerase.
Related PDB
Related UniProtKB P67910
[6]
Resource
Comments
Medline ID
PubMed ID 12137277
Journal Nat Prod Rep
Year 2002
Volume 19
Pages 261-77
Authors Samuel J, Tanner ME
Title Mechanistic aspects of enzymatic carbohydrate epimerization.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 15264802
Journal J Am Chem Soc
Year 2004
Volume 126
Pages 8878-9
Authors Read JA, Ahmed RA, Morrison JP, Coleman WG Jr, Tanner ME
Title The mechanism of the reaction catalyzed by ADP-beta-L-glycero-D-manno-heptose 6-epimerase.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 15823050
Journal Biochemistry
Year 2005
Volume 44
Pages 5907-15
Authors Morrison JP, Read JA, Coleman WG Jr, Tanner ME
Title Dismutase activity of ADP-L-glycero-D-manno-heptose 6-epimerase: evidence for a direct oxidation/reduction mechanism.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 15932222
Journal Org Lett
Year 2005
Volume 7
Pages 2457-60
Authors Read JA, Ahmed RA, Tanner ME
Title Efficient chemoenzymatic synthesis of ADP-D-glycero-beta-D-manno-heptose and a mechanistic study of ADP-L-glycero-D-manno-heptose 6-epimerase.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 17316025
Journal Biochemistry
Year 2007
Volume 46
Pages 3916-24
Authors Morrison JP, Tanner ME
Title A two-base mechanism for Escherichia coli ADP-L-glycero-D-manno-heptose 6-epimerase.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 20506248
Journal Protein Sci
Year 2010
Volume 19
Pages 1337-43
Authors Kowatz T, Morrison JP, Tanner ME, Naismith JH
Title The 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 PDB 2x6t 2x86
Related UniProtKB

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.

Created Updated
2004-04-05 2011-07-07