1EE1

CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE MOLECULE ATP, TWO MOLECULES DEAMIDO-NAD+ AND ONE MG2+ ION

Summary for 1EE1

• Entry DOI: 10.2210/pdb1ee1/pdb
• Related: 1IFX 1nsy
• Descriptor: NH(3)-DEPENDENT NAD(+) SYNTHETASE, MAGNESIUM ION, NICOTINIC ACID ADENINE DINUCLEOTIDE, ... (5 entities in total)
• Functional Keywords: lyase, amidotransferase, nh3 dependent, atp pyrophosphatase, ligase
• Biological source: Bacillus subtilis
• Total number of polymer chains: 2
• Total formula weight: 62470.31

Authors

Devedjiev, Y.,Symersky, J.,Singh, R.,Jedrzejas, M.,Brouillette, C.,Brouillette, W.,Muccio, D.,Chattopadhyay, D.,Delucas, L. (deposition date: 2000-01-28, release date: 2001-06-06, Last modification date: 2024-02-07)

Primary citation

Devedjiev, Y.,Symersky, J.,Singh, R.,Jedrzejas, M.,Brouillette, C.,Brouillette, W.,Muccio, D.,Chattopadhyay, D.,DeLucas, L.
Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis.
Acta Crystallogr.,Sect.D, 57:806-812, 2001

PubMed Abstract: The NH(3)-dependent NAD(+) synthetase (NADS) participates in the biosynthesis of nicotinamide adenine dinucleotide (NAD(+)) by transforming nicotinic acid adenine dinucleotide (NaAD) to NAD(+). The structural behavior of the active site, including stabilization of flexible loops 82-87 and 204-225, has been studied by determination of the crystal structures of complexes of NADS with natural substrates and a substrate analog. Both loops are stabilized independently of NaAD and solely from the ATP-binding site. Analysis of the binding contacts suggests that the minor loop 82-87 is stabilized primarily by a hydrogen bond with the adenine base of ATP. Formation of a coordination complex with Mg(2+) in the ATP-binding site may contribute to the stabilization of the major loop 204-225. The major loop has a role in substrate recognition and stabilization, in addition to the protection of the reaction intermediate described previously. A second and novel Mg(2+) position has been observed closer to the NaAD-binding site in the structure crystallized at pH 7.5, where the enzyme is active. This could therefore be the catalytically active Mg(2+).

PubMed: 11375500
DOI: 10.1107/S0907444901003523

Experimental method

X-RAY DIFFRACTION (2.06 Å)