1M5W

1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with 1-deoxy-D-xylulose phosphate

Summary for 1M5W

• Entry DOI: 10.2210/pdb1m5w/pdb
• Related: 1HO1 1HO4
• Descriptor: Pyridoxal phosphate biosynthetic protein pdxJ, 1-DEOXY-D-XYLULOSE-5-PHOSPHATE, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: tim barrel, protein-substrate complex, multi-binding states, biosynthetic protein
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P0A794
• Total number of polymer chains: 8
• Total formula weight: 212845.32

Authors

Yeh, J.I.,Du, S.,Pohl, E.,Cane, D.E. (deposition date: 2002-07-10, release date: 2003-07-15, Last modification date: 2024-02-14)

Primary citation

Yeh, J.I.,Du, S.,Pohl, E.,Cane, D.E.
Multistate Binding in Pyridoxine 5'-Phosphate Synthase: 1.96 A Crystal Structure in Complex with 1-deoxy-D-xylulose phosphate
Biochemistry, 41:11649-11657, 2002

PubMed Abstract: We report the 1.96 A crystal structure of pyridoxine 5'-phosphate synthase (PdxJ) in complex with 1-deoxy-D-xylulose phosphate (dXP). The octameric enzyme possesses eight distinct binding sites, and three different binding states are observed. The observation of these three states supports a mechanism in which precise conformational changes of a peptide loop and groups of active site residues modulate binding and specificity. The differences in protein conformation when one or two substrates are bound can be correlated with a condensation mechanism that leads productively to the formation of pyridoxine 5'-phosphate (PNP). "Snapshots" of the progression from the apo form to a singly occupied "transitional binding" state and, subsequently, to a fully occupied, reactive state are revealed and indicate how the enzyme structure can be related to a plausible catalytic mechanism and, moreover, to favorable energetics of reaction.

PubMed: 12269807
DOI: 10.1021/bi026292t

Experimental method

X-RAY DIFFRACTION (1.96 Å)