1VKL

RABBIT MUSCLE PHOSPHOGLUCOMUTASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural changes at the metal ion binding site during the phosphoglucomutase reaction.

Ray Jr., W.J.Post, C.B.Liu, Y.Rhyu, G.I.

(1993) Biochemistry 32: 48-57

  • DOI: 10.1021/bi00052a008
  • Primary Citation of Related Structures:  
    1VKL

  • PubMed Abstract: 
  • An electron density map of the reactive, Cd2+ form of crystalline phosphoglucomutase from X-ray diffraction studies shows that the enzymic phosphate donates a nonbridging oxygen to the ligand sphere of the bound metal ion, which appears to be tetracoordinate ...

    An electron density map of the reactive, Cd2+ form of crystalline phosphoglucomutase from X-ray diffraction studies shows that the enzymic phosphate donates a nonbridging oxygen to the ligand sphere of the bound metal ion, which appears to be tetracoordinate. 31P and 113Cd NMR spectroscopy are used to assess changes in the properties of bound Cd2+ produced by substrate/product and by substrate/product analog inhibitors. The approximately 50 ppm downfield shift of the 113Cd resonance on formation of the complex of dephosphoenzyme and glucose 1,6-bisphosphate is associated with the initial sugar-phosphate binding step and likely involves a change in the geometry of the coordinating ligands. This interpretation is supported by spectral studies involving various complexes of the active Co2+ and Ni(2+)-enzyme. In addition, there is a loss of the 31P-113Cd J coupling that characterizes the monophosphate complexes of the Cd2+ enzyme either during or immediately after the PO3- transfer step that produces the bisphosphate complex, indicating a further change at the metal binding site. The implications of these observations with respect to the PO3- transfer process in the phosphoglucomutase reaction are considered. The apparent plasticity of the ligand sphere of the active site metal ion in this system may allow a single metal ion to act as a chaperone for a nonbridging oxygen during PO3- transfer or to allow a change in metal ion coordination during catalysis. A general NMR line shape/chemical-exchange analysis for evaluating binding in protein-ligand systems when exchange is intermediate to fast on the NMR time scale is described. Its application to the present system involves multiple exchange sites that depend on a single binding rate, thereby adding further constraints to the analysis.


    Related Citations: 
    • The Crystal Structure of Muscle Phosphoglucomutase Refined at 2.7-Angstrom Resolution
      Dai, J.B., Liu, Y., Ray Junior, W.J., Konno, M.
      (1992) J Biol Chem 267: 6322
    • The Catalytic Activity of Muscle Phosphoglucomutase in the Crystalline Phase
      Ray Junior, W.J.
      (1986) J Biol Chem 261: 275
    • The Structure of Rabbit Muscle Phosphoglucomutase at Intermediate Resolution
      Lin, Z., Konno, M., Abad-Zapatero, C., Wierenga, R., Murthy, M.R., Ray Junior, W.J., Rossmann, M.G.
      (1986) J Biol Chem 261: 264

    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHOGLUCOMUTASEA, B561Oryctolagus cuniculusMutation(s): 0 
Gene Names: PGM1
EC: 5.4.2.2
UniProt
Find proteins for P00949 (Oryctolagus cuniculus)
Explore P00949 
Go to UniProtKB:  P00949
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, BL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.42α = 90
b = 174.42β = 90
c = 101.12γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-01-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance