2X86

AGME bound to ADP-B-mannose

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

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.

Kowatz, T., Morrison, J.P., Tanner, M.E., Naismith, J.H.

(2010) Protein Sci 19: 1337

  • DOI: 10.1002/pro.410
  • Primary Citation of Related Structures:  
    2X6T, 2X86

  • PubMed Abstract: 

    • Bacteria synthesize a wide array of unusual carbohydrate molecules, which they use in a variety of ways. The carbohydrate L-glycero-D-manno-heptose is an important component of lipopolysaccharide and is synthesized in a complex series of enzymatic steps. One step involves the epimerization at the C6'' position converting ADP-D-glycero-D-manno-heptose into ADP-L-glycero-D-manno-heptose ...

    Bacteria synthesize a wide array of unusual carbohydrate molecules, which they use in a variety of ways. The carbohydrate L-glycero-D-manno-heptose is an important component of lipopolysaccharide and is synthesized in a complex series of enzymatic steps. One step involves the epimerization at the C6'' position converting ADP-D-glycero-D-manno-heptose into ADP-L-glycero-D-manno-heptose. The enzyme responsible is a member of the short chain dehydrogenase superfamily, known as ADP-L-glycero-D-manno-heptose 6-epimerase (AGME). The structure of the enzyme was known but the arrangement of the catalytic site with respect to the substrate is unclear. We now report the structure of AGME bound to a substrate mimic, ADP-beta-D-mannose, which has the same stereochemical configuration as the substrate. The complex identifies the key residues and allows mechanistic insight into this novel enzyme.

    Organizational Affiliation: 

    Biomolecular Sciences Research Complex, The University of St Andrews, Fife KY16 9RH, United Kingdom.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADP-L-GLYCERO-D-MANNO-HEPTOSE-6-EPIMERASE
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
357Escherichia coliMutation(s): 1 
EC: 5.1.3.20
UniProt
Find proteins for P67911 (Escherichia coli O157:H7)
Explore P67911 
Go to UniProtKB:  P67911
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP67911
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP
Download Ideal Coordinates CCD File 
AB [auth L],
CA [auth D],
DB [auth M],
FA [auth E],
GB [auth N],
AB [auth L],
CA [auth D],
DB [auth M],
FA [auth E],
GB [auth N],
IA [auth F],
JB [auth O],
LA [auth G],
MB [auth P],
OA [auth H],
PB [auth Q],
RA [auth I],
SB [auth R],
U [auth A],
UA [auth J],
VB [auth S],
X [auth B],
XA [auth K],
YB [auth T],
Z [auth C]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N		 Ligand Interaction
ADP
Query on ADP
Download Ideal Coordinates CCD File 
AA [auth C],
BB [auth L],
DA [auth D],
EB [auth M],
GA [auth E],
AA [auth C],
BB [auth L],
DA [auth D],
EB [auth M],
GA [auth E],
HB [auth N],
JA [auth F],
KB [auth O],
MA [auth G],
NB [auth P],
PA [auth H],
QB [auth Q],
SA [auth I],
TB [auth R],
V [auth A],
VA [auth J],
WB [auth S],
Y [auth B],
YA [auth K],
ZB [auth T]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
BMA
Query on BMA
Download Ideal Coordinates CCD File 
AC [auth T],
BA [auth C],
CB [auth L],
EA [auth D],
FB [auth M],
AC [auth T],
BA [auth C],
CB [auth L],
EA [auth D],
FB [auth M],
HA [auth E],
IB [auth N],
KA [auth F],
LB [auth O],
NA [auth G],
OB [auth P],
QA [auth H],
RB [auth Q],
TA [auth I],
UB [auth R],
W [auth A],
WA [auth J],
XB [auth S],
ZA [auth K]
beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.074α = 90
b = 162.458β = 101.45
c = 185.027γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-06-28
    Changes: Data collection
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary