1gim Citations

Crystal structures of adenylosuccinate synthetase from Escherichia coli complexed with GDP, IMP hadacidin, NO3-, and Mg2+.

J. Mol. Biol. 264 1013-27 (1996)
Cited: 13 times
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Abstract

Crystal structures of adenylosuccinate synthetase from Esherichia coli complexed with Mg2+, IMP, GDP, NO3- and hadacidin at 298 and 100 K have been refined to R-factors of 0.188 and 0.206 against data to 2.8 A and 2.5 A resolution, respectively. Conformational changes of up to 9 A relative to the unligated enzyme occur in loops that bind to Mg2+, GDP, IMP and hadacidin. Mg2+ binds directly to GDP, NO3-, hadacidin and the protein, but is only five-coordinated. Asp13, which approaches, but does not occupy the sixth coordination site of Mg2+, hydrogen bonds to N1 of IMP. The nitrogen atom of NO3- is approximately 2.7 A from O6 of IMP, reflecting a strong electrostatic interaction between the electron-deficient nitrogen atom and the electron-rich O6. The spatial relationships between GDP, NO3- and Mg2+ suggest an interaction between the beta,gamma-bridging oxygen atom of GTP and Mg2+ in the enzyme-substrate complex. His41 hydrogen bonds to the beta-phosphate group of GDP and approaches bound NO3-. The aldehyde group of hadacidin coordinates to the Mg2+, while its carboxyl group interacts with backbone amide groups 299 to 303 and the side-chain of Arg303. The 5'-phosphate group of IMP interacts with Asn38, Thr129, Thr239 and Arg143 (from a monomer related by 2-fold symmetry). A mechanism is proposed for the two-step reaction governed by the synthetase, in which His41 and Asp13 are essential catalytic side-chains.

Articles - 1gim mentioned but not cited (3)

  1. Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties. Petrova NV, Wu CH. BMC Bioinformatics 7 312 (2006)
  2. Selective prediction of interaction sites in protein structures with THEMATICS. Wei Y, Ko J, Murga LF, Ondrechen MJ. BMC Bioinformatics 8 119 (2007)
  3. ResBoost: characterizing and predicting catalytic residues in enzymes. Alterovitz R, Arvey A, Sankararaman S, Dallett C, Freund Y, Sjölander K. BMC Bioinformatics 10 197 (2009)


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Articles citing this publication (8)

  1. Crystal structure of CapZ: structural basis for actin filament barbed end capping. Yamashita A, Maeda K, Maéda Y. EMBO J. 22 1529-1538 (2003)
  2. Protein-lipid interactions: correlation of a predictive algorithm for lipid-binding sites with three-dimensional structural data. Scott DL, Diez G, Goldmann WH. Theor Biol Med Model 3 17 (2006)
  3. Adenylosuccinate synthetase and adenylosuccinate lyase deficiencies trigger growth and infectivity deficits in Leishmania donovani. Boitz JM, Strasser R, Yates PA, Jardim A, Ullman B. J. Biol. Chem. 288 8977-8990 (2013)
  4. Unique kinetic mechanism of Plasmodium falciparum adenylosuccinate synthetase. Raman J, Mehrotra S, Anand RP, Balaram H. Mol. Biochem. Parasitol. 138 1-8 (2004)
  5. Structures of adenylosuccinate synthetase from Triticum aestivum and Arabidopsis thaliana. Prade L, Cowan-Jacob SW, Chemla P, Potter S, Ward E, Fonne-Pfister R. J. Mol. Biol. 296 569-577 (2000)
  6. Purification and characterization of recombinant Plasmodium falciparum adenylosuccinate synthetase expressed in Escherichia coli. Jayalakshmi R, Sumathy K, Balaram H. Protein Expr. Purif. 25 65-72 (2002)
  7. Cavitation as a mechanism of substrate discrimination by adenylosuccinate synthetases. Iancu CV, Zhou Y, Borza T, Fromm HJ, Honzatko RB. Biochemistry 45 11703-11711 (2006)
  8. 8-(4-Bromo-2,3-dioxobutylthio)guanosine 5'-triphosphate: a new affinity label for purine nucleotide sites in proteins. Lee P, Gorrell A, Fromm HJ, Colman RF. Arch. Biochem. Biophys. 372 205-213 (1999)


Related citations provided by authors (2)

  1. Refined Crystal Structures of Unligated Adenylosuccinate Synthetase from E.Coli. Silva MM, Poland BW, Hoffman CR, Fromm HJ, Honzatko RB J. Mol. Biol. 254 431- (1995)
  2. Crystal Structure of Adenylosuccinate Synthetase from E.Coli. Poland BW, Silva MM, Serra MA, Cho Y, Kim KH, Harris EM, Honzatko RB J. Biol. Chem. 268 25334- (1993)