5KGL

2.45A resolution structure of Apo independent phosphoglycerate mutase from C. elegans (orthorhombic form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases.

Yu, H.Dranchak, P.Li, Z.MacArthur, R.Munson, M.S.Mehzabeen, N.Baird, N.J.Battalie, K.P.Ross, D.Lovell, S.Carlow, C.K.Suga, H.Inglese, J.

(2017) Nat Commun 8: 14932-14932

  • DOI: 10.1038/ncomms14932
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycolytic interconversion of phosphoglycerate isomers is catalysed in numerous pathogenic microorganisms by a cofactor-independent mutase (iPGM) structurally distinct from the mammalian cofactor-dependent (dPGM) isozyme. The iPGM active site dynamic ...

    Glycolytic interconversion of phosphoglycerate isomers is catalysed in numerous pathogenic microorganisms by a cofactor-independent mutase (iPGM) structurally distinct from the mammalian cofactor-dependent (dPGM) isozyme. The iPGM active site dynamically assembles through substrate-triggered movement of phosphatase and transferase domains creating a solvent inaccessible cavity. Here we identify alternate ligand binding regions using nematode iPGM to select and enrich lariat-like ligands from an mRNA-display macrocyclic peptide library containing >10 12 members. Functional analysis of the ligands, named ipglycermides, demonstrates sub-nanomolar inhibition of iPGM with complete selectivity over dPGM. The crystal structure of an iPGM macrocyclic peptide complex illuminated an allosteric, locked-open inhibition mechanism placing the cyclic peptide at the bi-domain interface. This binding mode aligns the pendant lariat cysteine thiolate for coordination with the iPGM transition metal ion cluster. The extended charged, hydrophilic binding surface interaction rationalizes the persistent challenges these enzymes have presented to small-molecule screening efforts highlighting the important roles of macrocyclic peptides in expanding chemical diversity for ligand discovery.


    Organizational Affiliation

    National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.,IMCA-CAT Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA.,Division of Genome Biology, New England Biolabs, Ipswich, Massachusetts 01938, USA.,Department of Chemistry, Graduate School of Sciences, The University of Tokyo, Tokyo 113-0033, Japan.,National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.,Proton Structure Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, USA.,National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2,3-bisphosphoglycerate-independent phosphoglycerate mutase
A, B
552Caenorhabditis elegansMutation(s): 0 
Gene Names: ipgm-1
EC: 5.4.2.12
Find proteins for G5EFZ1 (Caenorhabditis elegans)
Go to UniProtKB:  G5EFZ1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.321α = 90.00
b = 98.852β = 90.00
c = 173.144γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-26
    Type: Database references