7KNF

1.80A resolution structure of independent Phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (Ce-1 NHOH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-activity relationship of ipglycermide binding to phosphoglycerate mutases.

Wiedmann, M.Dranchak, P.K.Aitha, M.Queme, B.Collmus, C.D.Kashipathy, M.M.Kanter, L.Lamy, L.Rogers, J.M.Tao, D.Battaile, K.P.Rai, G.Lovell, S.Suga, H.Inglese, J.

(2021) J Biol Chem 296: 100628-100628

  • DOI: 10.1016/j.jbc.2021.100628
  • Primary Citation of Related Structures:  
    7KNF, 7KNG

  • PubMed Abstract: 
  • Human phosphoglycerate mutase (dPGM) catalysis is dependent on a 2,3-bisphosphoglycerate cofactor, while the nonhomologous isozyme in many parasitic species is cofactor-independent (iPGM). This mechanistic and phylogenetic diversity offers an opportunity for selective pharmacologic targeting of glycolysis in disease-causing organisms ...

    Human phosphoglycerate mutase (dPGM) catalysis is dependent on a 2,3-bisphosphoglycerate cofactor, while the nonhomologous isozyme in many parasitic species is cofactor-independent (iPGM). This mechanistic and phylogenetic diversity offers an opportunity for selective pharmacologic targeting of glycolysis in disease-causing organisms. We previously discovered ipglycermide, a potent inhibitor of iPGM, from a large combinatorial cyclic peptide library. To fully delineate the ipglycermide pharmacophore, herein we construct a detailed structure-activity relationship using 280 substituted ipglycermide analogs. Binding affinities of these analogs to immobilized C. elegans iPGM, measured as fold-enrichment relative to the index residue by deep sequencing of an mRNA display library, illuminated the significance of each amino acid to the pharmacophore. Using co-crystal structures and binding kinetics, we show that the high affinity of ipglycermide for iPGM orthologs, from B. malayi, O. volvulus, D. immitis, and E. coli is achieved by a co-dependence between 1) the off-rate mediated by the macrocycle Cys14 thiolate coordination to an active-site Zn 2+ ion in the iPGM phosphatase domain, and 2) shape-complementarity surrounding the macrocyclic core at the phosphotransferase-phosphatase domain interface. Our results show that the high affinity binding of ipglycermide to iPGMs freezes these structurally dynamic enzymes into an inactive, stable complex.


    Organizational Affiliation

    National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA. Electronic address: jinglese@mail.nih.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2,3-bisphosphoglycerate-independent phosphoglycerate mutaseA, B538Caenorhabditis elegansMutation(s): 0 
Gene Names: ipgm-1F57B10.3
EC: 5.4.2.12
UniProt
Find proteins for G5EFZ1 (Caenorhabditis elegans)
Explore G5EFZ1 
Go to UniProtKB:  G5EFZ1
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DTY-ASP-TYR-PRO-GLY-ASP-HIS-CYS-TYR-LEU-TYR-GLY-THRC, D14Caenorhabditis elegansMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], O [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], K [auth B], L [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
HOA
Query on HOA

Download Ideal Coordinates CCD File 
P [auth C], Q [auth D]HYDROXYAMINE
H3 N O
AVXURJPOCDRRFD-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], M [auth B], N [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, BL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.669α = 90
b = 75.846β = 98.31
c = 100.424γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)United States1ZIATR000247
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM110761

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-04-21
    Changes: Database references
  • Version 1.2: 2021-07-14
    Changes: Database references