1YT5

Crystal structure of NAD kinase from Thermotoga maritima

Summary for 1YT5

• Entry DOI: 10.2210/pdb1yt5/pdb
• Related: 1SUW 1U0R 1U0T
• Descriptor: inorganic polyphosphate/ATP-NAD kinase, SULFATE ION (3 entities in total)
• Functional Keywords: domain 1: alpha/beta domain2: beta sandwich, structural genomics, psi, protein structure initiative, berkeley structural genomics center, bsgc, transferase
• Biological source: Thermotoga maritima
• Cellular location: Cytoplasm : Q9X255
• Total number of polymer chains: 4
• Total formula weight: 118851.45

Authors

Berkeley Structural Genomics Center (BSGC) (deposition date: 2005-02-09, release date: 2005-04-05, Last modification date: 2024-02-14)

Primary citation

Oganesyan, V.,Huang, C.,Adams, P.D.,Jancarik, J.,Yokota, H.A.,Kim, R.,Kim, S.H.
Structure of a NAD kinase from Thermotoga maritima at 2.3 A resolution.
Acta Crystallogr.,Sect.F, 61:640-646, 2005

PubMed Abstract: NAD kinase is the only known enzyme that catalyzes the formation of NADP, a coenzyme involved in most anabolic reactions and in the antioxidant defense system. Despite its importance, very little is known regarding the mechanism of catalysis and only recently have several NAD kinase structures been deposited in the PDB. Here, an independent investigation of the crystal structure of inorganic polyphosphate/ATP-NAD kinase, PPNK_THEMA, a protein from Thermotoga maritima, is reported at a resolution of 2.3 A. The crystal structure was solved using single-wavelength anomalous diffraction (SAD) data collected at the Se absorption-peak wavelength in a state in which no cofactors or substrates were bound. It revealed that the 258-amino-acid protein is folded into two distinct domains, similar to recently reported NAD kinases. The N-terminal alpha/beta-domain spans the first 100 amino acids and the last 30 amino acids of the polypeptide and has several topological matches in the PDB, whereas the other domain, which spans the middle 130 residues, adopts a unique beta-sandwich architecture and only appreciably matches the recently deposited PDB structures of NAD kinases.

PubMed: 16511117
DOI: 10.1107/S1744309105019780

Experimental method

X-RAY DIFFRACTION (2.3 Å)