PDBsum entry 1khf

Lyase

PDB id: 1khf

Contents

Protein chain

603 a.a. *

Ligands

PEP

EDO ×2

Metals

_MN

_NA

Waters ×164

* Residue conservation analysis

PDB id:

1khf

Name:

Lyase

Title:

Pepck complex with pep

Structure:

Phosphoenolpyruvate carboxykinase, cytosolic (gtp). Chain: a. Synonym: phosphoenolpyruvate carboxylase, pepck, pepck-c. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pck1. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.02Å R-factor: 0.186 R-free: 0.244

Authors:

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

Key ref:

P.Dunten et al. (2002). Crystal structure of human cytosolic phosphoenolpyruvate carboxykinase reveals a new GTP-binding site. J Mol Biol, 316, 257-264. PubMed id: 11851336 DOI: 10.1006/jmbi.2001.5364

Date:

29-Nov-01 Release date: 27-Feb-02

Protein chain

P35558  (PCKGC_HUMAN) -  Phosphoenolpyruvate carboxykinase, cytosolic [GTP] from Homo sapiens

Seq: 622 a.a.

Struc: 603 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.2.7.11.- - ?????
• Enzyme class 3: E.C.4.1.1.32 - phosphoenolpyruvate carboxykinase (GTP).
• Reaction: oxaloacetate + GTP = phosphoenolpyruvate + GDP + CO2

oxaloacetate + GTP = phosphoenolpyruvate (Bound ligand (Het Group name = EDO) matches with 40.00% similarity) + GDP + CO2 (Bound ligand (Het Group name = PEP) corresponds exactly)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1006/jmbi.2001.5364

J Mol Biol 316:257-264 (2002)

PubMed id: 11851336

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

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

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.

Selected figure(s)

Figure 2.
Figure 2. Interactions between the base and sugar of the non-hydrolyzable GTP analog and the enzyme. The two water molecules mediating hydrogen bonds to the protein are shown as red spheres.

Figure 3.
Figure 3. Comparison of the GTP-dependent and ATP-dependent PEPCK structures. (a) Ribbon representation of the human enzyme with metal ions and non-hydrolyzable GTP shown in ball-and-stick form. (b) The E. coli enzyme with bound metal ions and ATP shown in the same orientation to highlight the similarity of the fold. (c) The active site of the human enzyme with bound non-hydrolyzable GTP. The Mg and Mn ions are shown as purple spheres and water molecules are shown as red spheres. (d) Corresponding view of the active site of the E. coli enzyme complexed with ATP taken from the Protein Data Bank, entry 1aq2[6]. A bound molecule of pyruvate marks the location of the PEP site. The indicated torsion angle (O4'-C1'-N9-C4) is 57° (syn) for bound ATP, versus 236° (anti) for the GTP bound to the human enzyme. Atoms in the Figures are colored by type, with C, N, O, S, and P atoms in green, dark blue, red, yellow, and light blue, respectively.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 316, 257-264) copyright 2002.

Figures were selected by an automated process.