1KHE

PEPCK complex with nonhydrolyzable GTP analog, MAD data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of human cytosolic phosphoenolpyruvate carboxykinase reveals a new GTP-binding site.

Dunten, P.Belunis, C.Crowther, R.Hollfelder, K.Kammlott, U.Levin, W.Michel, H.Ramsey, G.B.Swain, A.Weber, D.Wertheimer, S.J.

(2002) J Mol Biol 316: 257-264

  • DOI: 10.1006/jmbi.2001.5364
  • Primary Citation of Related Structures:  
    1KHE, 1KHB, 1KHG, 1KHF

  • PubMed Abstract: 
  • We report crystal structures of the human enzyme phosphoenolpyruvate carboxykinase (PEPCK) with and without bound substrates. These structures are the first to be determined for a GTP-dependent PEPCK, and provide the first view of a novel GTP-binding site unique to the GTP-dependent PEPCK family ...

    We report crystal structures of the human enzyme phosphoenolpyruvate carboxykinase (PEPCK) with and without bound substrates. These structures are the first to be determined for a GTP-dependent PEPCK, and provide the first view of a novel GTP-binding site unique to the GTP-dependent PEPCK family. Three phenylalanine residues form the walls of the guanine-binding pocket on the enzyme's surface and, most surprisingly, one of the phenylalanine side-chains contributes to the enzyme's specificity for GTP. PEPCK catalyzes the rate-limiting step in the metabolic pathway that produces glucose from lactate and other precursors derived from the citric acid cycle. Because the gluconeogenic pathway contributes to the fasting hyperglycemia of type II diabetes, inhibitors of PEPCK may be useful in the treatment of diabetes.


    Organizational Affiliation

    Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA. pete.dunten@roche.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphoenolpyruvate Carboxykinase, cytosolic (GTP)A625Homo sapiensMutation(s): 25 
Gene Names: PCK1PEPCK1
EC: 4.1.1.32 (PDB Primary Data), 2.7.11 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P35558 (Homo sapiens)
Explore P35558 
Go to UniProtKB:  P35558
PHAROS:  P35558
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCP (Subject of Investigation/LOI)
Query on GCP

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.174 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.386α = 88.36
b = 60.54β = 70.39
c = 61.833γ = 72.37
Software Package:
Software NamePurpose
SHARPphasing
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description