6GPJ

Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4F-Man


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Parsimonious Mechanism of Sugar Dehydration by Human GDP-Mannose-4,6-dehydratase.

Pfeiffer, M.Johansson, C.Krojer, T.Kavanagh, K.L.Oppermann, U.Nidetzky, B.

(2019) Acs Catalysis 9: 2962-2968

  • DOI: 10.1021/acscatal.9b00064
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Biosynthesis of 6-deoxy sugars, including l-fucose, involves a mechanistically complex, enzymatic 4,6-dehydration of hexose nucleotide precursors as the first committed step. Here, we determined pre- and postcatalytic complex structures of the human ...

    Biosynthesis of 6-deoxy sugars, including l-fucose, involves a mechanistically complex, enzymatic 4,6-dehydration of hexose nucleotide precursors as the first committed step. Here, we determined pre- and postcatalytic complex structures of the human GDP-mannose 4,6-dehydratase at atomic resolution. These structures together with results of molecular dynamics simulation and biochemical characterization of wildtype and mutant enzymes reveal elusive mechanistic details of water elimination from GDP-mannose C5″ and C6″, coupled to NADP-mediated hydride transfer from C4″ to C6″. We show that concerted acid-base catalysis from only two active-site groups, Tyr 179 and Glu 157 , promotes a syn 1,4-elimination from an enol (not an enolate) intermediate. We also show that the overall multistep catalytic reaction involves the fewest position changes of enzyme and substrate groups and that it proceeds under conserved exploitation of the basic (minimal) catalytic machinery of short-chain dehydrogenase/reductases.


    Organizational Affiliation

    Austrian Centre of Industrial Biotechnology, 8010 Graz, Austria.,Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, 79085 Freiburg, Germany.,Botnar Research Centre, University of Oxford, Oxford OX3 7LD, United Kingdom.,Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, 8010 Graz, Austria.,Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GDP-mannose 4,6 dehydratase
A, D, C, B
352Homo sapiensMutation(s): 0 
Gene Names: GMDS
EC: 4.2.1.47
Find proteins for O60547 (Homo sapiens)
Go to Gene View: GMDS
Go to UniProtKB:  O60547
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A, B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B, C, D
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
G4F
Query on G4F

Download SDF File 
Download CCD File 
A, B, C, D
[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S},6~{R})-5-fluoranyl-6-(hydroxymethyl)-3,4-bis(oxidanyl)oxan-2-yl] hydrogen phosphate
C16 H24 F N5 O15 P2
LDMYSLGOFVDHNN-YVXBHLEUSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
B, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 92.080α = 90.00
b = 114.438β = 90.00
c = 140.536γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
DIALSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2019-04-24
    Type: Data collection, Database references