1Y3H

Crystal Structure of Inorganic Polyphosphate/ATP-NAD kinase from Mycobacterium tuberculosis

Summary for 1Y3H

• Entry DOI: 10.2210/pdb1y3h/pdb
• Related: 1Y3I
• Descriptor: Inorganic polyphosphate/ATP-NAD kinase (2 entities in total)
• Functional Keywords: nad kinase, polyphosphate, nad, atp, transferase
• Biological source: Mycobacterium tuberculosis
• Cellular location: Cytoplasm: P0A5S6
• Total number of polymer chains: 2
• Total formula weight: 65911.42

Authors

Mori, S.,Yamasaki, M.,Maruyama, Y.,Momma, K.,kawai, S.,Hashimoto, W.,Mikami, B.,Murata, K. (deposition date: 2004-11-24, release date: 2005-01-18, Last modification date: 2024-05-29)

Primary citation

Mori, S.,Yamasaki, M.,Maruyama, Y.,Momma, K.,Kawai, S.,Hashimoto, W.,Mikami, B.,Murata, K.
NAD-binding mode and the significance of intersubunit contact revealed by the crystal structure of Mycobacterium tuberculosis NAD kinase-NAD complex
BIOCHEM.BIOPHYS.RES.COMMUN., 327:500-508, 2005

PubMed Abstract: NAD kinase is a key enzyme in NADP biosynthesis. We solved the crystal structure of polyphosphate/ATP-NAD kinase from Mycobacterium tuberculosis (Ppnk) complexed with NAD (Ppnk-NAD) at 2.6A resolution using apo-Ppnk structure solved in this work, and revealed the details of the structure and NAD-binding site. Superimposition of tertiary structures of apo-Ppnk and Ppnk-NAD demonstrated a substantial conformational difference in a loop (Ppnk-flexible loop). As a quaternary structure, these Ppnk structures exhibited tetramer as in solution condition. Notably, the Ppnk-flexible loop was involved in the intersubunit contact and probably related to the NAD-binding of the other subunit. Furthermore, the two residues (Asp189, His226) substantially contributed to creating NAD-binding site on the other subunit. The two residues and the residues involved in NAD-binding were conserved. However, residues corresponding to the Ppnk-flexible loop were not conserved, making us to speculate that the Ppnk-flexible loop may be Ppnk-specific.

PubMed: 15629142
DOI: 10.1016/j.bbrc.2004.11.163

Experimental method

X-RAY DIFFRACTION (2.8 Å)