4M51

Crystal structure of amidohydrolase nis_0429 (ser145ala mutant) from nitratiruptor sp. sb155-2

Summary for 4M51

• Entry DOI: 10.2210/pdb4m51/pdb
• Related: 3V7P
• Descriptor: Amidohydrolase family protein, BENZOIC ACID, SULFATE ION, ... (6 entities in total)
• Functional Keywords: hydrolase, amidohydrolase, iron binding site, enzyme function initiative, efi, structural genomics
• Biological source: Nitratiruptor sp. SB155-2
• Total number of polymer chains: 1
• Total formula weight: 48910.28

Authors

Patskovsky, Y.,Toro, R.,Gobble, A.,Raushel, F.M.,Almo, S.C.,Enzyme Function Initiative (EFI) (deposition date: 2013-08-07, release date: 2013-09-04, Last modification date: 2024-10-30)

Primary citation

Goble, A.M.,Toro, R.,Li, X.,Ornelas, A.,Fan, H.,Eswaramoorthy, S.,Patskovsky, Y.,Hillerich, B.,Seidel, R.,Sali, A.,Shoichet, B.K.,Almo, S.C.,Swaminathan, S.,Tanner, M.E.,Raushel, F.M.
Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes.
Biochemistry, 52:6525-6536, 2013

PubMed Abstract: Proteins of unknown function belonging to cog1816 and cog0402 were characterized. Sav2595 from Steptomyces avermitilis MA-4680, Acel0264 from Acidothermus cellulolyticus 11B, Nis0429 from Nitratiruptor sp. SB155-2 and Dr0824 from Deinococcus radiodurans R1 were cloned, purified, and their substrate profiles determined. These enzymes were previously incorrectly annotated as adenosine deaminases or chlorohydrolases. It was shown here that these enzymes actually deaminate 6-aminodeoxyfutalosine. The deamination of 6-aminodeoxyfutalosine is part of an alternative menaquinone biosynthetic pathway that involves the formation of futalosine. 6-Aminodeoxyfutalosine is deaminated by these enzymes with catalytic efficiencies greater than 10(5) M(-1) s(-1), Km values of 0.9-6.0 μM, and kcat values of 1.2-8.6 s(-1). Adenosine, 2'-deoxyadenosine, thiomethyladenosine, and S-adenosylhomocysteine are deaminated at least an order of magnitude slower than 6-aminodeoxyfutalosine. The crystal structure of Nis0429 was determined and the substrate, 6-aminodeoxyfutalosine, was positioned in the active site on the basis of the presence of adventitiously bound benzoic acid. In this model, Ser-145 interacts with the carboxylate moiety of the substrate. The structure of Dr0824 was also determined, but a collapsed active site pocket prevented docking of substrates. A computational model of Sav2595 was built on the basis of the crystal structure of adenosine deaminase and substrates were docked. The model predicted a conserved arginine after β-strand 1 to be partially responsible for the substrate specificity of Sav2595.

PubMed: 23972005
DOI: 10.1021/bi400750a

Experimental method

X-RAY DIFFRACTION (1.08 Å)