3BI0

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a transition state analog of Glu-Glu


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of interactions between human glutamate carboxypeptidase II and its substrate analogs

Barinka, C.Hlouchova, K.Rovenska, M.Majer, P.Dauter, M.Hin, N.Ko, Y.S.Tsukamoto, T.Slusher, B.S.Konvalinka, J.Lubkowski, J.

(2008) J Mol Biol 376: 1438-1450

  • DOI: 10.1016/j.jmb.2007.12.066
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Human glutamate carboxypeptidase II (GCPII) is involved in neuronal signal transduction and intestinal folate absorption by means of the hydrolysis of its two natural substrates, N-acetyl-aspartyl-glutamate and folyl-poly-gamma-glutamates, respective ...

    Human glutamate carboxypeptidase II (GCPII) is involved in neuronal signal transduction and intestinal folate absorption by means of the hydrolysis of its two natural substrates, N-acetyl-aspartyl-glutamate and folyl-poly-gamma-glutamates, respectively. During the past years, tremendous efforts have been made toward the structural analysis of GCPII. Crystal structures of GCPII in complex with various ligands have provided insight into the binding of these ligands, particularly to the S1' site of the enzyme. In this article, we have extended structural characterization of GCPII to its S1 site by using dipeptide-based inhibitors that interact with both S1 and S1' sites of the enzyme. To this end, we have determined crystal structures of human GCPII in complex with phosphapeptide analogs of folyl-gamma-glutamate, aspartyl-glutamate, and gamma-glutamyl-glutamate, refined at 1.50, 1.60, and 1.67 A resolution, respectively. The S1 pocket of GCPII could be accurately defined and analyzed for the first time, and the data indicate the importance of Asn519, Arg463, Arg534, and Arg536 for recognition of the penultimate (i.e., P1) substrate residues. Direct interactions between the positively charged guanidinium groups of Arg534 and Arg536 and a P1 moiety of a substrate/inhibitor provide mechanistic explanation of GCPII preference for acidic dipeptides. Additionally, observed conformational flexibility of the Arg463 and Arg536 side chains likely regulates GCPII affinity toward different inhibitors and modulates GCPII substrate specificity. The biochemical experiments assessing the hydrolysis of several GCPII substrate derivatives modified at the P1 position, also included in this report, further complement and extend conclusions derived from the structural analysis. The data described here form an a solid foundation for the structurally aided design of novel low-molecular-weight GCPII inhibitors and imaging agents.


    Organizational Affiliation

    Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. cyril@ncifcrf.gov



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate carboxypeptidase 2
A
709Homo sapiensMutation(s): 0 
Gene Names: FOLH1FOLHNAALAD1PSMPSMAGIG27
EC: 3.4.17.21
Find proteins for Q04609 (Homo sapiens)
Go to UniProtKB:  Q04609
NIH Common Fund Data Resources
PHAROS  Q04609
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BIX
Query on BIX

Download CCD File 
A
(2S)-2-{[(S)-[(3S)-3-amino-3-carboxypropyl](hydroxy)phosphoryl]methyl}pentanedioic acid
C10 H18 N O8 P
YLHAQDFYEKJARV-RQJHMYQMSA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BIXIC50:  14   nM  Binding MOAD
EPEIC50:  14   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.405α = 90
b = 130.797β = 90
c = 159.14γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance