Crystal structure of human protein N-terminal glutamine amidohydrolase, an initial component of the N-end rule pathway

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Park, Mi Seul ^a   Bitto, Eduard ^b   Kim, Kyung Rok ^a   Bingman, Craig A ^c   Miller, Mitchell D ^d   Kim, Hyun Jung ^e   Han, Byung Woo ^a   Phillips, George N ^c,d  

^a Seoul National University   (South Korea)

^b GEORGIAN COURT UNIVERSITY   (United States)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

^d RICE UNIVERSITY   (United States)

^e Chung Ang University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC ACID; CYSTEINE; GLUTAMIC ACID; GLUTAMINASE; GLUTAMINE; HISTIDINE; HUMAN N TERMINAL GLUTAMINE AMIDOHYDROLASE 1; PROTEIN GLUTAMINE GAMMA GLUTAMYLTRANSFERASE; UNCLASSIFIED DRUG; AMIDASE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; DEAMINATION; ENZYME ACTIVE SITE; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; MOLECULAR DOCKING; PROTEIN PROTEIN INTERACTION; STRUCTURE ANALYSIS; CHEMISTRY; HUMAN; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; STRUCTURE ACTIVITY RELATION; X RAY CRYSTALLOGRAPHY;

AMIDOHYDROLASES; CRYSTALLOGRAPHY, X-RAY; HUMANS; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84910032182     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0111142     Document Type: Article

References (30)

1. Mogk A, Schmidt R, Bukau B (2007) The N-end rule pathway for regulated proteolysis: prokaryotic and eukaryotic strategies. Trends Cell Biol 17:165-172.
2. Lecker SH, Goldberg AL, Mitch WE (2006) Protein degradation by the ubiquitin-proteasome pathway in normal and disease states. J Am Soc Nephrol 17:1807-1819.
3. Knop M, Schiffer HH, Rupp S, Wolf DH (1993) Vacuolar/lysosomal proteolysis: proteases, substrates, mechanisms. Curr Opin Cell Biol 5:990-996.
4. Bachmair A, Finley D, Varshavsky A (1986) In vivo half-life of a protein is a function of its amino-terminal residue. Science 234:179-186.
5. Tasaki T, Kwon YT (2007) The mammalian N-end rule pathway: new insights into its components and physiological roles. Trends Biochem Sci 32:520-528.
6. Baker RT, Varshavsky A (1995) Yeast N-terminal amidase. A new enzyme and component of the N-end rule pathway. J Biol Chem 270:12065-12074.
7. Kwon YT, Balogh SA, Davydov IV, Kashina AS, Yoon JK, et al. (2000) Altered activity, social behavior, and spatial memory in mice lacking the NTAN1p amidase and the asparagine branch of the N-end rule pathway. Mol Cell Biol 20:4135-4148.
8. Wang H, Piatkov KI, Brower CS, Varshavsky A (2009) Glutamine-specific N-terminal amidase, a component of the N-end rule pathway. Mol Cell 34:686-695.
9. Hwang CS, Shemorry A, Varshavsky A (2009) Two proteolytic pathways regulate DNA repair by cotargeting the Mgt1 alkylguanine transferase. Proc Natl Acad Sci U S A 106:2142-2147.
10. Eisele F, Wolf DH (2008) Degradation of misfolded protein in the cytoplasm is mediated by the ubiquitin ligase Ubr1. FEBS Lett 582:4143-4146.
11. Kwon YT, Xia Z, An JY, Tasaki T, Davydov IV, et al. (2003) Female lethality and apoptosis of spermatocytes in mice lacking the UBR2 ubiquitin ligase of the N-end rule pathway. Mol Cell Biol 23:8255-8271.
12. Ditzel M, Wilson R, Tenev T, Zachariou A, Paul A, et al. (2003) Degradation of DIAP1 by the N-end rule pathway is essential for regulating apoptosis. Nat Cell Biol 5:467-473.
13. Thao S, Zhao Q, Kimball T, Steffen E, Blommel PG, et al. (2004) Results from high-throughput DNA cloning of Arabidopsis thaliana target genes using sitespecific recombination. J Struct Funct Genomics 5:267-276.
14. Sreenath HK, Bingman CA, Buchan BW, Seder KD, Burns BT, et al. (2005) Protocols for production of selenomethionine-labeled proteins in 2-L polyethylene terephthalate bottles using auto-induction medium. Protein Expr Purif 40:256-267.
15. Jeon WB, Aceti DJ, Bingman CA, Vojtik FC, Olson AC, et al. (2005) Highthroughput purification and quality assurance of Arabidopsis thaliana proteins for eukaryotic structural genomics. J Struct Funct Genomics 6:143-147.
16. Studier FW (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41:207-234.
17. Bricogne G, Vonrhein C, Flensburg C, Schiltz M, Paciorek W (2003) Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Crystallogr D Biol Crystallogr 59:2023-2030.
18. Cowtan KD, Zhang KY (1999) Density modification for macromolecular phase improvement. Prog Biophys Mol Biol 72:245-270.
19. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126-2132.
20. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53:240-255.
21. Laskowski RA, Moss DS, Thornton JM (1993) Main-chain bond lengths and bond angles in protein structures. J Mol Biol 231:1049-1067.
22. Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, et al. (2003) Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins 50:437-450.
23. Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455-461.
24. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, et al. (2009) AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 30:2785-2791.
25. The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC.
26. Holm L, Rosenstrom P (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38:W545-549.
27. Hashizume R, Maki Y, Mizutani K, Takahashi N, Matsubara H, et al. (2011) Crystal structures of protein glutaminase and its pro forms converted into enzyme-substrate complex. J Biol Chem 286:38691-38702.
28. Bhaskaran SS, Stebbins CE (2012) Structure of the catalytic domain of the Salmonella virulence factor SseI. Acta Crystallogr D Biol Crystallogr 68:1613-1621.
29. Chatterjee D, Boyd CD, O'Toole GA, Sondermann H (2012) Structural characterization of a conserved, calcium-dependent periplasmic protease from Legionella pneumophila. J Bacteriol 194:4415-4425.
30. Choi WS, Jeong BC, Joo YJ, Lee MR, Kim J, et al. (2010) Structural basis for the recognition of N-end rule substrates by the UBR box of ubiquitin ligases. Nat Struct Mol Biol 17:1175-1181.