6GPK

Crystal structure of human GDP-D-mannose 4,6-dehydratase (E157Q) in complex with GDP-Man


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 

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 Catal 9: 2962-2968

  • DOI: 10.1021/acscatal.9b00064
  • Structures With Same Primary Citation

  • 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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GDP-mannose 4,6 dehydratase
A, B, C, D
373Homo sapiensMutation(s): 1 
Gene Names: GMDS
EC: 4.2.1.47
Find proteins for O60547 (Homo sapiens)
Go to UniProtKB:  O60547
NIH Common Fund Data Resources
PHAROS  O60547
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download CCD File 
A, B, C, D
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
GDD
Query on GDD

Download CCD File 
A, B, C, D
GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
C16 H25 N5 O16 P2
MVMSCBBUIHUTGJ-GDJBGNAASA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.73α = 90
b = 114.532β = 90
c = 140.061γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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