Structures of N-acetylornithine transcarbamoylase from Xanthomonas campestris complexed with substrates and substrate analogs imply mechanims for substrate binding and catalysis

Proteins: Structure, Function and Genetics

Volumn 64, Issue 2, 2006, Pages 532-542

  Shi, Dashuang ^a,c   Yu, Xiaolin ^a   Roth, Lauren ^b   Morizono, Hiroki ^a   Tuchman, Mendel ^a   Allewell, Norma M ^b  

^a CHILDREN'S NATIONAL MEDICAL CENTER   (United States)

^b Bldg 142   (United States)

^c CHILDREN S RESEARCH INSTITUTE   (United States)

Author keywords

Arginine biosynthesis; Crystal structure; Domain movement; Novel enzyme; Plant pathogen

Indexed keywords

ARGININE; ASPARTATE CARBAMOYLTRANSFERASE; CARBAMOYL PHOSPHATE; CARBAMOYLTRANSFERASE; N ACETYLORNITHINE TRANSCARBAMOYLASE; NORVALINE; UNCLASSIFIED DRUG;

AMINO ACID SYNTHESIS; ARTICLE; BACTERIUM; CARBAMOYLATION; CATALYSIS; COMPLEX FORMATION; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; NONHUMAN; PRIORITY JOURNAL; XANTHOMONAS CAMPESTRIS;

BINDING SITES; CARBOXYL AND CARBAMOYL TRANSFERASES; CATALYSIS; CLONING, MOLECULAR; LIGANDS; MODELS, STATISTICAL; MOLECULAR CONFORMATION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; STEREOISOMERISM; SUBSTRATE SPECIFICITY; XANTHOMONAS CAMPESTRIS;

BACTERIA (MICROORGANISMS); XANTHOMONAS CAMPESTRIS;

EID: 33745604557     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21013     Document Type: Article

References (40)

1. Cunin R, Glansdorff N, Pierard A, Stalon V. Biosynthesis and metabolism of arginine in bacteria. Microbiol Rev 1986;50:314-352.
2. Shi D, Morizono H, Yu X, Tong L, Allewell NM, Tuchman M. Human ornithine transcarbamoylase: crystallographic insights into substrate recognition and conformational changes. Biochem J 2001;354:501-509.
3. Shi D, Gallegos R, DePonte J 3rd, et al. Crystal structure of a transcarbamoylase-like protein from the anaerobic bacterium Bacteroides fragilis at 2.0 Å resolution. J Mol Biol 2002;320:899-908.
4. da Silva AC, Ferro JA, Reinach FC, et al. Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 2002;417:459-463.
5. da Silva FR, Vettore AL, Kemper EL, Leite A, Arruda P. Fastidian gum: the Xylella fastidiosa exopolysaccharide possibly involved in bacterial pathogenicity. EMS Microbiol Lett 2001;203:165-171.
6. Miki T, Kuwahara T, Nakayama H, et al. Simultaneous detection of Bacteroides fragilis group species by leuB-directed PCR. J Med Invest 2005;52:101-108.
7. Sanz M, Lau L, Herrera D, Morillo JM, Silva A. Methods of detection of Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis and Tannerella forsythensis in periodontal microbiology, with special emphasis on advanced molecular techniques: a review. J Clin Periodontol 2004;31:1034-1047.
8. Shi D, Morizono H, Yu X, et al. Crystal structure of N-acetylornithine transcarbamoylase from Xanthomonas campestris: a novel enzyme in a new arginine biosynthetic pathway found in several eubacteria. J Biol Chem 2005;280:14366-14369.
9. Morizono H, Cabrera-Luque J, Shi D, et al. Acetylornithine transcarbamylase: a novel enzyme in arginine biosynthesis. J Bacteriol 2006;188:2974-2982.
10. Naumoff DG, Xu Y, Glansdorff N, Labedan B. Retrieving sequences of enzymes experimentally characterized but erroneously annotated: the case of the putrescine carbamoyltransferase. BMC Genomics 2004;5:52.
11. Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 1997;276:307-326.
12. Brünger AT, Adams PD, Clore GM, et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 1998;54:905-921.
13. Brünger AT. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature (Lond) 1992;355:472-475.
14. Jones TA, Zou JY, Cowan SW, Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 1991;47:110-119.
15. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PRO-CHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993;26:283-291.
16. δ-(N′- sulfodiaminophosphinyl)-L-ornithine, a true transition state analogue? Crystal structure and implications for catalytic mechanism. J Biol Chem 2000;275:20012-20019.
17. Schuettelkopf AW, van Aalten DMF. PRODRG - a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr 2004;60:1355-1363.
18. Kraulis PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;24:946-950.
19. Merritt EA, Murphy ME. RasterSD Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr D Biol Crystallogr 1994;50:869-873.
20. DeLano WL. The PyMOL Molecular Graphics System. 2002. http://www.pymol.org.
21. Wallace AC, Laskowski RA, Thornron JM. LIGPLOT: a program to generate schematic diagram of protein-ligand interactions. Protein Eng 1995;8:127-134.
22. Lipscomb WN. Aspartate transcarbamoylase from Escherichia coli: activity and regulation. Adv Enzymol Relat Areas Mol Biol 1994;68:67-151.
23. Allewell NM, Shi D, Morizono H, Tuchman M. Molecular recognition by ornithine and aspartate transcarbamoylases. Acc Chem Res 1999;32:885-894.
24. Ha Y, McCann MT, Tuchman M, Allewell NM, Substrate-induced conformational change in a trimeric ornithine transcarbamoylase. Proc Natl Acad Sci USA 1997;94:9550-9555.
25. Shi D, Morizono H, Ha Y, Aoyagi M, Tuchman M, Allewell NM. 1.85 Å resolution crystal structure of human ornithine transcarbamoylase complexed with N-phosphonacetyl-L-ornithine. J Biol Chem 1998;273:34247-34254.
26. Shi D, Morizono H, Aoyagi M, Tuchman M, Allewell NM. Crystal structure of human ornithine transcarbamoylase complexed with carbamoyl phosphate and L-norvaline at 1.9 Å resolution. Proteins 2000;39:271-277.
27. Massant J, Wouters J, Glansdorff N. Refined structure of Pyrococcus furiosus ornithine carbamoyltransferase at 1.87 Å. Acta Crystallogr D Biol Crystallogr 2003;59:2140-2149.
28. Van Boxstael S, Cunin R, Khan S, Maes D. Aspartate transcarbamoylase from the hyperthermophilic archaeon Pyrococcus abyssi: thermostability and 1.8 Å resolution crystal structure of the catalytic subunit complexed with the bisubstrate analogue N-phosphonacetyl-L-aspartate. J Mol Biol 2003;326:203-216.
29. Huang J, Lipscomb WN. Aspartate transcarbamoylase (ATCase) of Escherichia coli: a new crystalline R-state bound to PALA, or to product analogues citrate and phosphate. Biochemistry 2004;43:6415-6421.
30. Wang J, Stieglitz KA, Cardia JP, Kantrowitz ER. Structural basis for ordered substrate binding and cooperativity in aspartate transcarbamoylase. Proc Natl Acad Sci USA 2005;102:8881-8886.
31. Mosqueda G, Van den Broeck G, Saucedo O, Bailey AM, Alvarez-Morales A, Herrera-Estrella L. Isolation and characterization of the gene from Pseudomonas syringae pv. phaseolicola encoding the phaseolotoxin-insensitive ornithine carbamoyltransferase. Mol Gen Genet 1990;222:461-466.
32. Williamson CL, Lake MR, Slocum RD. Isolation and characterization of a cDNA encoding a pea ornithine transcarbamoylase (argF) and comparison with other transcarbamoylases. Plant Mol Biol 1996;31:1087-1092.
33. Morizono H, Tuchman M, Rajagopal BS, et al. Expression, purification and kinetic characterization of wild-type human ornithine transcarbamoylase and a recurrent mutant that produces 'late onset' hyperammonaemia. Biochem J 1997;322:625-631.
34. Gouaux JE, Krause KL, Lipscomb WN. The catalytic mechanism of Escherichia coli aspartate carbamoyltransferase: a molecular modelling study. Biochem Biophys Res Commun 1987;142:893-897.
35. Jin L, Stec B, Kantrowitz ER. A cis-proline to alanine mutant of E. coli aspartate transcarbamoylase: kinetic studies and three-dimensional crystal structures. Biochemistry 2000;39:8058-8066.
36. Porter RW, Modebe MO, Stark GR. Aspartate transcarbamoylase. Kinetic studies of the catalytic subunit. J Biol Chem 1969;244:1846-1859.
37. Legrain C, Stalon V. Ornithine carbamoyltransferase from Escherichia coli W. Purification, structure and steady-state kinetic analysis. Eur J Biochem 1976;63:289-301.
38. McDowall S, van Heeswijck R, Hoogenraad N. Site-directed mutagenesis of Arg 60 and Cys 271 in ornithine transcarbamylase from rat liver. Protein Eng 1990;4:73-77.
39. Huang J, Lipscomb WN. Products in the T-state of aspartate transcarbamoylase: crystal structure of the phosphate and N-carbamyl-L-aspartate ligated enzyme. Biochemistry 2004;43:6422-6426.
40. Huang J, Lipscomb WN. T-state active site of aspartate transcarbamylase: crystal structure of the carbamyl phosphate and L-alanosine ligated enzyme. Biochemistry 2006;45:346-352.