Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 Å resolution

Proteins: Structure, Function and Genetics

Volumn 64, Issue 3, 2006, Pages 808-813

  Xu, Qingping ^a,b   Schwarzenbacher, Robert ^a,c   Sri Krishna, S ^a,c   McMullan, Daniel ^a,d   Agarwalla, Sanjay ^a,d   Quijano, Kevin ^a,d   Abdubek, Polat ^a,d   Ambing, Eileen ^a,d   Axelrod, Herbert ^a,b   Biorac, Tanya ^a,d   Canaves, Jaume M ^a,c   Chiu, Hsiu Ju ^a,b   Elsliger, Marc André ^a,e   Grittini, Carina ^a,e   Grzeeknik, Slawomir K ^a,c   DiDonato, Michael ^a,d   Hale, Joanna ^a,d   Hampton, Eric ^a,d   Han, Gye Won ^a,e   Haugen, Justin ^a,d   Hornsby, Michael ^a,d   Jaroszewski, Lukasz ^a,c   Klock, Heath E ^a,d   Knuth, Mark W ^a,d   Koesema, Eric ^a,d   Kreusch, Andreas ^a,d   Kuhn, Peter ^a,e   Miller, Mitchell D ^a,b   Moy, Kin ^a,e   Nigoghossian, Edward ^a,d   Paulsen, Jessica ^a,d   Reyes, Ron ^a,b   Rife, Chris ^a,b   Spraggon, Glen ^a,d   Stevens, Raymond C ^a,e   Van Den Bedem, Henry ^a,b   Velasquez, Jeff ^a,e   White, Aprilfawn ^a,d   Wolf, Guenter ^a,b   Hodgson, Keith O ^a,b   Wooley, John ^a,c   Deacon, Ashley M ^a,b   Godzik, Adam ^a,c   Lesley, Scott A ^a,d   Wilson, Ian A ^a,e   more..

^a STANFORD UNIVERSITY   (United States)

^b SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

^e SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACIREDUCTONE DIOXYGENASE; DIOXYGENASE; UNCLASSIFIED DRUG;

CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME STRUCTURE; MOLECULAR WEIGHT; MOUSE; MOUSE STRAIN; MUS MUSCULUS; NONHUMAN; NOTE; NUCLEOTIDE SEQUENCE; OPTICAL RESOLUTION; PRIORITY JOURNAL; PROTEIN FAMILY; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; CRYSTALLIZATION; DATABASES, PROTEIN; DIOXYGENASES; METALS; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY;

MUS MUSCULUS;

EID: 33746239542     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20947     Document Type: Note

References (25)

1. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR. The Pfam protein families database. Nucleic Acids Res 2004;32:D138-D141.
2. Dunwell JM, Khuri S, Gane PJ. Microbial relatives of the seed storage proteins of higher plants: conservation of structure and diversification of function during evolution of the cupin superfamily. Microbiol Mol Biol Rev 2000;64:153-179.
3. Dai Y, Wensink PC, Abeles RH. One protein, two enzymes. J Biol Chem 1999;274:1193-1195.
4. Dai Y, Pochapsky TC, Abeles RH. Mechanistic studies of two dioxygenases in the methionine salvage pathway of Klebsiella pneumonias. Biochemistry 2001;40:6379-6387.
5. Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elsliger MA, Wooley J, Taylor SS, Hodgson KO, Wilson IA, Schultz PG, Stevens RC. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci U S A 2002;99:11664-11669.
6. Davis IW, Murray LW, Richardson JS, Richardson DC. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 2004;32: W615-W619.
7. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
8. Pochapsky TC, Pochapsky SS, Ju T, Mo H, Al-Mjeni F, Maroney MJ. Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae. Nat Struct Biol 2002;9: 966-972.
9. Holm L, Sander C. Dali: a network tool for protein structure comparison. Trends Biochem Sci 1995;20:478-480.
10. Ko TP, Day J, McPherson A. The refined structure of canavalin from jack bean in two crystal forms at 2.1 and 2.0 A resolution. Acta Crystallogr D Biol Crystallogr 2000;56(Pt 4):411-420.
11. McMullan D, Schwarzenbacher R, Jaroszewski L, von Delft F, Klock HE, Vincent J, Quijano K, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Karlak C, Koesema E, Kreusch A, Kuhn P, Levin I, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Reyes R, Rezezadeh F, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Lesley SA, Wilson IA. Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 Å resolution. Proteins 2004;56:615-618.
12. Jaroszewski L, Li W, Godzik A. In search for more accurate alignments in the twilight zone. Protein Sci 2002;11:1702-1713.
13. Jaroszewski L, Schwarzenbacher R, von Delft F, McMullan D, Brinen LS, Canaves JM, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Levin I, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Reyes R, Rezezadeh F, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 Å resolution. Proteins 2004;56:611-614.
14. Schwarzenbacher R, von Delft F, Jaroszewski L, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Karlak C, Hock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a putative oxalate decarboxylase (TM1287) from Thermotoga maritima at 1.95 Å resolution. Proteins 2004;56:392-395.
15. Santarsiero BD, Yegian DT, Lee CC, Spraggon G, Gu J, Scheibe D, Uber DC, Cornell EW, Nordmeyer RA, Kolbe WF, Jin J, Jones AL, Jaklevic JM, Schultz PG, Stevens RC. An approach to rapid protein crystallization using nanodroplets. J Appl Crystallogr 2002;35:278-281.
16. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 1994;50:760-763.
17. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J Appl Cryst 1993;26:795-800.
18. Terwilliger TC, Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr 1999;55:849-861.
19. Cohen SX, Morris RJ, Fernandez FJ, Ben Jelloul M, Kakaris M, Parthasarathy V, Lamzin VS, Kleywegt GJ, Perrakis A. Towards complete validated models in the next generation of ARP/wARP. Acta Crystallogr D Biol Crystallogr 2004;60:2222-2229.
20. Jones TA, Zou JY, Cowan SW, Kjeldgaard. 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.
21. Winn MD, Murshudov GN, Papiz MZ. Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol 2003;374:300-321.
22. Yang H, Guranovic V, Dutta S, Feng Z, Berman HM, Westbrook JD. Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. Acta Crystallogr D Biol Crystallogr 2004;60:1833-1839.
23. Vaguine AA, Richelle J, Wodak SJ. SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr D Biol Crystallogr 1999;55:191-205.
24. Vriend G. WHAT IF: a molecular modeling and drug design program. J Mol Graph 1990;8:52-56, 29.
25. Tickle IJ, Laskowski RA, Moss DS. Error estimates of protein structure coordinates and deviations from standard geometry by full-matrix refinement of gammaB- and betaB2-crystallin. Acta Crystallogr D Biol Crystallogr 1998;54:243-252.