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Regulation of the intersubunit ammonia tunnel in Mycobacterium tuberculosis glutamine-dependent NAD+ synthetase.

Chuenchor W, Doukov TI, Resto M, Chang A, Gerratana B
Biochem J 443 417-26 (2012)
Related entries: 3sdb, 3seq, 3sez, 3szg

Cited: 10 times
EuropePMC logo PMID: 22280445

Abstract

Glutamine-dependent NAD+ synthetase is an essential enzyme and a validated drug target in Mycobacterium tuberculosis (mtuNadE). It catalyses the ATP-dependent formation of NAD+ from NaAD+ (nicotinic acid-adenine dinucleotide) at the synthetase active site and glutamine hydrolysis at the glutaminase active site. An ammonia tunnel 40 Å (1 Å=0.1 nm) long allows transfer of ammonia from one active site to the other. The enzyme displays stringent kinetic synergism; however, its regulatory mechanism is unclear. In the present paper, we report the structures of the inactive glutaminase C176A variant in an apo form and in three synthetase-ligand complexes with substrates (NaAD+/ATP), substrate analogue {NaAD+/AMP-CPP (adenosine 5'-[α,β-methylene]triphosphate)} and intermediate analogues (NaAD+/AMP/PPi), as well as the structure of wild-type mtuNadE in a product complex (NAD+/AMP/PPi/glutamate). This series of structures provides snapshots of the ammonia tunnel during the catalytic cycle supported also by kinetics and mutagenesis studies. Three major constriction sites are observed in the tunnel: (i) at the entrance near the glutaminase active site; (ii) in the middle of the tunnel; and (iii) at the end near the synthetase active site. Variation in the number and radius of the tunnel constrictions is apparent in the crystal structures and is related to ligand binding at the synthetase domain. These results provide new insight into the regulation of ammonia transport in the intermolecular tunnel of mtuNadE.

Articles - 3syt mentioned but not cited (2)

  1. Different ways to transport ammonia in human and Mycobacterium tuberculosis NAD+ synthetases. Chuenchor W, Doukov TI, Chang KT, Resto M, Yun CS, Gerratana B. Nat Commun 11 16 (2020)
  2. Streptococcus pyogenes quinolinate-salvage pathway-structural and functional studies of quinolinate phosphoribosyl transferase and NH3 -dependent NAD+ synthetase. Booth WT, Morris TL, Mysona DP, Shah MJ, Taylor LK, Karlin TW, Clary K, Majorek KA, Offermann LR, Chruszcz M. FEBS J 284 2425-2441 (2017)


Reviews citing this publication (1)

  1. A structural perspective on the PP-loop ATP pyrophosphatase family. Fellner M, Hausinger RP, Hu J. Crit Rev Biochem Mol Biol 53 607-622 (2018)

Articles citing this publication (7)

  1. Evidence for hysteretic substrate channeling in the proline dehydrogenase and Δ1-pyrroline-5-carboxylate dehydrogenase coupled reaction of proline utilization A (PutA). Moxley MA, Sanyal N, Krishnan N, Tanner JJ, Becker DF. J Biol Chem 289 3639-3651 (2014)
  2. Glutamine versus ammonia utilization in the NAD synthetase family. De Ingeniis J, Kazanov MD, Shatalin K, Gelfand MS, Osterman AL, Sorci L. PLoS One 7 e39115 (2012)
  3. Biochemical and structural characterization of oxygen-sensitive 2-thiouridine synthesis catalyzed by an iron-sulfur protein TtuA. Chen M, Asai SI, Narai S, Nambu S, Omura N, Sakaguchi Y, Suzuki T, Ikeda-Saito M, Watanabe K, Yao M, Shigi N, Tanaka Y. Proc Natl Acad Sci U S A 114 4954-4959 (2017)
  4. Bi-allelic Mutations in NADSYN1 Cause Multiple Organ Defects and Expand the Genotypic Spectrum of Congenital NAD Deficiency Disorders. Szot JO, Campagnolo C, Cao Y, Iyer KR, Cuny H, Drysdale T, Flores-Daboub JA, Bi W, Westerfield L, Liu P, Leung TN, Choy KW, Chapman G, Xiao R, Siu VM, Dunwoodie SL. Am J Hum Genet 106 129-136 (2020)
  5. Design, synthesis, and evaluation of substituted nicotinamide adenine dinucleotide (NAD+) synthetase inhibitors as potential antitubercular agents. Wang X, Ahn YM, Lentscher AG, Lister JS, Brothers RC, Kneen MM, Gerratana B, Boshoff HI, Dowd CS. Bioorg Med Chem Lett 27 4426-4430 (2017)
  6. Kinetics and structural features of dimeric glutamine-dependent bacterial NAD+ synthetases suggest evolutionary adaptation to available metabolites. Santos ARS, Gerhardt ECM, Moure VR, Pedrosa FO, Souza EM, Diamanti R, Högbom M, Huergo LF. J Biol Chem 293 7397-7407 (2018)
  7. NAD+ Synthetase is Required for Free-living and Symbiotic Nitrogen Fixation in the Actinobacterium Frankia casuarinae. Kucho KI, Asukai K, Nguyen TV. Microbes Environ 38 (2023)


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