Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 69.71 kDa 
• Atom Count: 4826 
• Modelled Residue Count: 603 
• Deposited Residue Count: 625 
• Unique protein chains: 1

1KHG

PEPCK

• PDB DOI: 10.2210/pdb1KHG/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-11-29 Released: 2002-02-27 
• Deposition Author(s): Dunten, P., Belunis, C., Crowther, R., Hollfelder, K., Kammlott, U., Levin, W., Michel, H., Ramsey, G.B., Swain, A., Weber, D., Wertheimer, S.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.281 
• R-Value Work: 0.185 
• R-Value Observed: 0.190 

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

• PubMed: 11851336 
• DOI: 10.1006/jmbi.2001.5364
• Primary Citation of Related Structures:  
  1KHB, 1KHE, 1KHF, 1KHG


• 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. 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. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate carboxykinase, cytosolic (GTP)	A	625	Homo sapiens	Mutation(s): 3  Gene Names: PCK1, PEPCK1 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 GTEx:  ENSG00000124253

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.281 
• R-Value Work: 0.185 
• R-Value Observed: 0.190 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.388	α = 88.69
b = 60.872	β = 70.13
c = 61.974	γ = 72.37

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-29 
• Released Date: 2002-02-27 
Deposition Author(s): Dunten, P., Belunis, C., Crowther, R., Hollfelder, K., Kammlott, U., Levin, W., Michel, H., Ramsey, G.B., Swain, A., Weber, D., Wertheimer, S.J.

Revision History  

• 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