PDBsum entry 1kf0

Transferase

PDB id: 1kf0

Contents

Protein chain

416 a.a. *

Ligands

3PG

ACP

Metals

_MG

Waters ×81

* Residue conservation analysis

PDB id:

1kf0

Name:

Transferase

Title:

Crystal structure of pig muscle phosphoglycerate kinase ternary complex with amp-pcp and 3pg

Structure:

Phosphoglycerate kinase. Chain: a. Ec: 2.7.2.3

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Other_details: muscle

Resolution:

2.50Å R-factor: 0.173 R-free: 0.252

Authors:

Z.Kovari,B.Flachner,G.Naray-Szabo,M.Vas

Key ref:

Z.Kovári et al. (2002). Crystallographic and thiol-reactivity studies on the complex of pig muscle phosphoglycerate kinase with ATP analogues: correlation between nucleotide binding mode and helix flexibility. Biochemistry, 41, 8796-8806. PubMed id: 12102622 DOI: 10.1021/bi020210j

Date:

19-Nov-01 Release date: 24-Jul-02

Protein chain

Q7SIB7  (PGK1_PIG) -  Phosphoglycerate kinase 1 from Sus scrofa

Seq: 417 a.a.

Struc: 416 a.a.*

* PDB and UniProt seqs differ at 14 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.7.2.3 - phosphoglycerate kinase.
• Pathway: Calvin Cycle (carbon fixation stages)
• Reaction: (2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP

(2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP (Bound ligand (Het Group name = ACP) matches with 81.25% similarity)

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

Added reference

DOI no: 10.1021/bi020210j

Biochemistry 41:8796-8806 (2002)

PubMed id: 12102622

Crystallographic and thiol-reactivity studies on the complex of pig muscle phosphoglycerate kinase with ATP analogues: correlation between nucleotide binding mode and helix flexibility.

Z.Kovári, B.Flachner, G.Náray-Szabó, M.Vas.

ABSTRACT

Crystal structure of the ternary complex of pig muscle phosphoglycerate kinase (PGK) with the substrate 3-phosphoglycerate (3-PG) and the Mg(2+) complex of beta,gamma-methylene-adenosine-5'-triphosphate (AMP-PCP), a nonreactive analogue of the nucleotide substrate, MgATP, has been determined by X-ray diffraction at 2.5 A resolution. The overall structure of the protein exhibits an open conformation, similar to that of the previously determined ternary complex of the pig muscle enzyme with beta,gamma-imido-adenosine-5'-triphosphate (AMP-PNP) in place of AMP-PCP (May, Vas, Harlos, and Blake (1996) Proteins 24, 292-303). The orientation and details of interactions of the nucleotide phosphates, however, show marked differences. The beta-phosphate is linked to the conserved Asp 218, i.e., to the N-terminus of helix 8, through the Mg(2+) ion; the previously observed interactions of the metal complex of AMP-PNP or ADP with the conserved Asn 336 and the N-terminus of helix 13 are completely absent. These structural differences are maintained themselves in solution studies. Inhibition and binding experiments show a slightly weaker interaction of PGK with MgAMP-PCP than with MgAMP-PNP: at pH 7.5, the K(d) values are 1.07 +/- 0.18 and 0.41 +/- 0.08 mM, respectively. The difference is further enhanced by 3-PG: the K(d) values are 2.80 +/- 0.66 and 0.68 +/- 0.11 mM, respectively. Thus, the previously observed weakening effect of 3-PG on nucleotide binding (Merli, Szilágyi, Flachner, Rossi, and Vas (2002) Biochemistry 41, 111-119) is more pronounced with MgAMP-PCP. The discordance between substrate analogues also shows up in thiol reactivity studies. In their binary complexes, both ATP analogues protect the fast-reacting thiols of PGK in helix 13 against modification to similar extent. In their ternary complexes, however, which also contain bound 3-PG, the protective effect of MgAMP-PCP, but not of MgAMP-PNP, is largely abolished. This indicates a much smaller effect of MgAMP-PCP on the conformation of helix 13, which is in good correlation with its altered mode of phosphate binding and the ensuing increase in the flexibility of helix 13, as shown by elevated crystallographic B-factors. The possible existence of alternative site(s) for binding of the nucleotide phosphates may have functional relevance.