2H5A

Complex of the enzyme PMM/PGM with xylose 1-phosphate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

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This is version 1.5 of the entry. See complete history. 


Literature

Complexes of the enzyme phosphomannomutase/phosphoglucomutase with a slow substrate and an inhibitor.

Regni, C., Shackelford, G.S., Beamer, L.J.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 722-726

  • DOI: https://doi.org/10.1107/S1744309106025887
  • Primary Citation of Related Structures:  
    2H4L, 2H5A

  • PubMed Abstract: 

    Two complexes of the enzyme phosphomannomutase/phosphoglucomutase (PMM/PGM) from Pseudomonas aeruginosa with a slow substrate and with an inhibitor have been characterized by X-ray crystallography. Both ligands induce an interdomain rearrangement in the enzyme that creates a highly buried active site. Comparisons with enzyme-substrate complexes show that the inhibitor xylose 1-phosphate utilizes many of the previously observed enzyme-ligand interactions. In contrast, analysis of the ribose 1-phosphate complex reveals a combination of new and conserved enzyme-ligand interactions for binding. The ability of PMM/PGM to accommodate these two pentose phosphosugars in its active site may be relevant for future efforts towards inhibitor design.

    • Organizational Affiliation: 

    Department of Structural Biology, St Jude Children's Research Hospital, 332 North Lauderdale M/S 311, Memphis, TN 38105, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphomannomutase/phosphoglucomutaseA [auth X]463Pseudomonas aeruginosaMutation(s): 1 
Gene Names: algC
EC: 5.4.2.8 (PDB Primary Data), 5.4.2.2 (PDB Primary Data)
UniProt
Find proteins for P26276 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P26276 
Go to UniProtKB:  P26276
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26276
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP		A [auth X]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
X1P PDBBind:  2H5A Kd: 8000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.008α = 90
b = 74.551β = 90
c = 86.091γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.5: 2024-11-06
    Changes: Data collection, Database references, Structure summary