3NL9

Crystal structure of a putative NTP pyrophosphohydrolase (Exig_1061) from EXIGUOBACTERIUM SP. 255-15 at 1.78 A resolution

Replaces:  3MQUReplaces:  2RFP

Summary for 3NL9

• Entry DOI: 10.2210/pdb3nl9/pdb
• Descriptor: putative NTP pyrophosphohydrolase, 1,2-ETHANEDIOL (3 entities in total)
• Functional Keywords: structural genomics, joint center for structural genomics, jcsg, protein structure initiative, psi-2, hydrolase
• Biological source: Exiguobacterium sibiricum 255-15 (Exiguobacterium sp. 255-15)
• Total number of polymer chains: 1
• Total formula weight: 19521.20

Authors

Joint Center for Structural Genomics (JCSG) (deposition date: 2010-06-21, release date: 2010-07-21, Last modification date: 2024-10-09)

Primary citation

Han, G.W.,Elsliger, M.A.,Yeates, T.O.,Xu, Q.,Murzin, A.G.,Krishna, S.S.,Jaroszewski, L.,Abdubek, P.,Astakhova, T.,Axelrod, H.L.,Carlton, D.,Chen, C.,Chiu, H.J.,Clayton, T.,Das, D.,Deller, M.C.,Duan, L.,Ernst, D.,Feuerhelm, J.,Grant, J.C.,Grzechnik, A.,Jin, K.K.,Johnson, H.A.,Klock, H.E.,Knuth, M.W.,Kozbial, P.,Kumar, A.,Lam, W.W.,Marciano, D.,McMullan, D.,Miller, M.D.,Morse, A.T.,Nigoghossian, E.,Okach, L.,Reyes, R.,Rife, C.L.,Sefcovic, N.,Tien, H.J.,Trame, C.B.,van den Bedem, H.,Weekes, D.,Hodgson, K.O.,Wooley, J.,Deacon, A.M.,Godzik, A.,Lesley, S.A.,Wilson, I.A.
Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.
Acta Crystallogr.,Sect.F, 66:1237-1244, 2010

PubMed Abstract: The crystal structure of a putative NTPase, YP_001813558.1 from Exiguobacterium sibiricum 255-15 (PF09934, DUF2166) was determined to 1.78 Å resolution. YP_001813558.1 and its homologs (dimeric dUTPases, MazG proteins and HisE-encoded phosphoribosyl ATP pyrophosphohydrolases) form a superfamily of all-α-helical NTP pyrophosphatases. In dimeric dUTPase-like proteins, a central four-helix bundle forms the active site. However, in YP_001813558.1, an unexpected intertwined swapping of two of the helices that compose the conserved helix bundle results in a `linked dimer' that has not previously been observed for this family. Interestingly, despite this novel mode of dimerization, the metal-binding site for divalent cations, such as magnesium, that are essential for NTPase activity is still conserved. Furthermore, the active-site residues that are involved in sugar binding of the NTPs are also conserved when compared with other α-helical NTPases, but those that recognize the nucleotide bases are not conserved, suggesting a different substrate specificity.

PubMed: 20944217
DOI: 10.1107/S1744309110025534

Experimental method

X-RAY DIFFRACTION (1.78 Å)