1MV8

1.55 A crystal structure of a ternary complex of GDP-mannose dehydrogenase from Psuedomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The crystal structure of GDP-mannose dehydrogenase: A key enzyme in alginate biosynthesis of P. aeruginosa

Snook, C.F.Tipton, P.A.Beamer, L.J.

(2003) Biochemistry 42: 4658-4668

  • DOI: 10.1021/bi027328k
  • Primary Citation of Related Structures:  
    1MFZ, 1MV8, 1MUU

  • PubMed Abstract: 
  • The enzyme GMD from Pseudomonas aeruginosa catalyzes the committed step in the synthesis of the exopolysaccharide alginate. Alginate is a major component of P. aeruginosa biofilms that protect the bacteria from the host immune response and antibiotic therapy ...

    The enzyme GMD from Pseudomonas aeruginosa catalyzes the committed step in the synthesis of the exopolysaccharide alginate. Alginate is a major component of P. aeruginosa biofilms that protect the bacteria from the host immune response and antibiotic therapy. The 1.55 A crystal structure of GMD in ternary complex with its cofactor NAD(H) and product GDP-mannuronic acid reveals that the enzyme forms a domain-swapped dimer with two polypeptide chains contributing to each active site. The extensive dimer interface provides multiple opportunities for intersubunit communication. Comparison of the GMD structure with that of UDP-glucose dehydrogenase reveals the structural basis of sugar binding specificity that distinguishes these two related enzyme families. The high-resolution structure of GMD provides detailed information on the active site of the enzyme and a template for structure-based inhibitor design.


    Related Citations: 
    • Allosterism and cooperativity in Pseudomonas aeruginosa GDP-mannose dehydrogenase
      Naught, L.E., Gilbert, S., Imhoff, R., Snook, C., Beamer, L., Tipton, P.
      (2002) Biochemistry 41: 9637

    Organizational Affiliation

    Department of Biochemistry, 117 Schweitzer Hall, University of Missouri-Columbia, Columbia, Missouri 65211, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GDP-mannose 6-dehydrogenaseA, B, C, D436Pseudomonas aeruginosaMutation(s): 0 
Gene Names: algD
EC: 1.1.1.132
UniProt
Find proteins for P11759 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P11759 
Go to UniProtKB:  P11759
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranoseE, F2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
G [auth A], J [auth B], K [auth C], O [auth D]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
GDX
Query on GDX

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], P [auth D], Q [auth D]GUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE), P'-D-MANNOPYRANOSYL ESTER
C16 H23 N5 O17 P2
DNBSDUDYNPJVCN-ZXTXFPBHSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
N [auth C](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
L [auth C], M [auth C]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
E, FsucroseOligosaccharide /  Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.472α = 90
b = 82.472β = 90
c = 309.893γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-06
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2014-11-12
    Changes: Structure summary
  • Version 1.4: 2018-02-14
    Changes: Experimental preparation
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary