2CIR

Structure-based functional annotation: Yeast ymr099c codes for a D- hexose-6-phosphate mutarotase. Complex with glucose-6-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure-based functional annotation: yeast ymr099c codes for a D-hexose-6-phosphate mutarotase.

Graille, M.Baltaze, J.P.Leulliot, N.Liger, D.Quevillon-Cheruel, S.van Tilbeurgh, H.

(2006) J Biol Chem 281: 30175-30185

  • DOI: 10.1074/jbc.M604443200
  • Primary Citation of Related Structures:  
    2CIS, 2CIR, 2CIQ

  • PubMed Abstract: 
  • Despite the generation of a large amount of sequence information over the last decade, more than 40% of well characterized enzymatic functions still lack associated protein sequences. Assigning protein sequences to documented biochemical functions is an interesting challenge ...

    Despite the generation of a large amount of sequence information over the last decade, more than 40% of well characterized enzymatic functions still lack associated protein sequences. Assigning protein sequences to documented biochemical functions is an interesting challenge. We illustrate here that structural genomics may be a reasonable approach in addressing these questions. We present the crystal structure of the Saccharomyces cerevisiae YMR099cp, a protein of unknown function. YMR099cp adopts the same fold as galactose mutarotase and shares the same catalytic machinery necessary for the interconversion of the alpha and beta anomers of galactose. The structure revealed the presence in the active site of a sulfate ion attached by an arginine clamp made by the side chain from two strictly conserved arginine residues. This sulfate is ideally positioned to mimic the phosphate group of hexose 6-phosphate. We have subsequently successfully demonstrated that YMR099cp is a hexose-6-phosphate mutarotase with broad substrate specificity. We solved high resolution structures of some substrate enzyme complexes, further confirming our functional hypothesis. The metabolic role of a hexose-6-phosphate mutarotase is discussed. This work illustrates that structural information has been crucial to assign YMR099cp to the orphan EC activity: hexose-phosphate mutarotase.


    Organizational Affiliation

    Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, CNRS UMR8619, F-91405 Orsay Cedex, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEXOSE-6-PHOSPHATE MUTAROTASEA297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YMR099CYM6543.06C
EC: 5.1.3.15
UniProt
Find proteins for Q03161 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03161 
Go to UniProtKB:  Q03161
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BG6
Query on BG6

Download Ideal Coordinates CCD File 
B [auth A]6-O-phosphono-beta-D-glucopyranose
C6 H13 O9 P
NBSCHQHZLSJFNQ-VFUOTHLCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
AL-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BG6Kd:  200000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.63α = 90
b = 157.067β = 90
c = 104.024γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-12
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Database references, Structure summary, Version format compliance
  • Version 1.2: 2018-03-07
    Changes: Database references, Source and taxonomy
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary