1KBL

PYRUVATE PHOSPHATE DIKINASE

Summary for 1KBL

• Entry DOI: 10.2210/pdb1kbl/pdb
• Related: 1DIK
• Descriptor: PYRUVATE PHOSPHATE DIKINASE, AMMONIUM ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: transferase, phosphotransferase, kinase
• Biological source: Clostridium symbiosum
• Total number of polymer chains: 1
• Total formula weight: 97138.50

Authors

Herzberg, O.,Chen, C.C.,Liu, S. (deposition date: 2001-11-06, release date: 2002-01-30, Last modification date: 2023-08-16)

Primary citation

Herzberg, O.,Chen, C.C.,Liu, S.,Tempczyk, A.,Howard, A.,Wei, M.,Ye, D.,Dunaway-Mariano, D.
Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis
Biochemistry, 41:780-787, 2002

PubMed Abstract: Crystals of pyruvate phosphate dikinase in complex with a substrate analogue inhibitor, phosphonopyruvate (K(i) = 3 microM), have been obtained in the presence of Mg(2+). The structure has been determined and refined at 2.2 A resolution, revealing that the Mg(2+)-bound phosphonopyruvate binds in the alpha/beta-barrel's central channel, at the C-termini of the beta-strands. The mode of binding resembles closely the previously proposed PEP substrate binding mode, inferred by the homology of the structure (but not sequence homology) to pyruvate kinase. Kinetic analysis of site-directed mutants, probing residues involved in inhibitor binding, showed that all mutations resulted in inactivation, confirming the key role that these residues play in catalysis. Comparison between the structure of the PPDK-phosphonopyruvate complex and the structures of two complexes of pyruvate kinase, one with Mg(2+)-bound phospholactate and the other with Mg(2+)-oxalate and ATP, revealed that the two enzymes share some key features that facilitate common modes of substrate binding. There are also important structural differences; most notably, the machinery for acid/base catalysis is different.

PubMed: 11790099
DOI: 10.1021/bi011799+

Experimental method

X-RAY DIFFRACTION (1.94 Å)