Structure of human aspartyl aminopeptidase complexed with substrate analogue: Insight into catalytic mechanism, substrate specificity and M18 peptidase family

BMC Structural Biology

Volumn 12, Issue , 2012, Pages

  Chaikuad, Apirat ^a   Pilka, Ewa S ^a   De Riso, Antonio ^b   Von Delft, Frank ^a   Kavanagh, Kathryn L ^a   Vénien Bryan, Catherine ^b   Oppermann, Udo ^a,c   Yue, Wyatt W ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c NIHR OXFORD BIOMEDICAL RESEARCH CENTRE   (United Kingdom)

Author keywords

Aspartyl aminopeptidase; Dodecameric tetrahedron; Domain swapping; M18 peptidase; Metalloprotease

Indexed keywords

AMINO ACID; ASPARTIC ACID BETA HYDROXAMIC ACID; ASPARTYL AMINOPEPTIDASE; METALLOPROTEINASE; METALLOPROTEINASE 18; METALLOPROTEINASE 42; UNCLASSIFIED DRUG; ZINC;

ARTICLE; CATALYSIS; CRYSTAL STRUCTURE; ELECTRON MICROSCOPY; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME SPECIFICITY; ENZYME STRUCTURE; LIGAND BINDING;

AMINO ACID SEQUENCE; BACTERIA; BIOCATALYSIS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; GLUTAMYL AMINOPEPTIDASE; HUMANS; METALS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, TERTIARY; STATIC ELECTRICITY; SUBSTRATE SPECIFICITY;

BACTERIA (MICROORGANISMS); MAMMALIA;

EID: 84862491849     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-12-14     Document Type: Article

References (37)

1. Aminopeptidases: structure and function. Taylor A, FASEB J 1993 7 2 290 298 8440407
2. Metallo-aminopeptidase inhibitors. Mucha A, Drag M, Dalton JP, Kafarski P, Biochimie 2010 92 11 1509 1529 10.1016/j.biochi.2010.04.026 20457213
3. cDNA cloning and expression of human glutamyl aminopeptidase (aminopeptidase A). Li L, Wang J, Cooper MD, Genomics 1993 17 3 657 664 10.1006/geno.1993.1386 8244382
4. Brain aminopeptidases and hypertension. Banegas I, Prieto I, Vives F, Alba F, de Gasparo M, Segarra AB, Hermoso F, Duran R, Ramirez M, J Renin Angiotensin Aldosterone Syst 2006 7 3 129 134 10.3317/jraas.2006.021 17094048
5. Brain renin-angiotensin-a new look at an old system. Wright JW, Harding JW, Prog Neurobiol 2011 95 1 49 67 10.1016/j.pneurobio.2011.07.001 21777652
6. Purification, characterization, and cloning of a cytosolic aspartyl aminopeptidase. Wilk S, Wilk E, Magnusson RP, J Biol Chem 1998 273 26 15961 15970 10.1074/jbc.273.26.15961 9632644
7. Identification of yeast aspartyl aminopeptidase gene by purifying and characterizing its product from yeast cells. Yokoyama R, Kawasaki H, Hirano H, FEBS J 2006 273 1 192 198 10.1111/j.1742-4658.2005.05057.x 16367759
8. Efficient production and partial characterization of aspartyl aminopeptidase from Aspergillus oryzae. Kusumoto KI, Matsushita-Morita M, Furukawa I, Suzuki S, Yamagata Y, Koide Y, Ishida H, Takeuchi M, Kashiwagi Y, J Appl Microbiol 2008 105 5 1711 1719 10.1111/j.1365-2672.2008.03889.x 18828788
9. Aspartyl aminopeptidase, encoded by an evolutionarily conserved syntenic gene, is colocalized with its cluster in secretory granules of pancreatic islet cells. Cai WW, Wang L, Chen Y, Biosci Biotechnol Biochem 74 10 2050 2055
10. Subcellular distribution of membrane-bound aminopeptidases in the human and rat brain. Larrinaga G, Callado LF, Agirregoitia N, Varona A, Gil J, Neurosci Lett 2005 383 1-2 136 140 15936526
11. Chondrocyte-specific microRNA-140 regulates endochondral bone development and targets Dnpep to modulate bone morphogenetic protein signaling. Nakamura Y, Inloes JB, Katagiri T, Kobayashi T, Mol Cell Biol 31 14 3019 3028
12. MEROPS: the peptidase database. Rawlings ND, Tolle DP, Barrett AJ, MEROPS, Nucleic Acids Res 2004 32 Database issue 160 D164 14681384
13. Metalloaminopeptidases: common functional themes in disparate structural surroundings. Lowther WT, Matthews BW, Chem Rev 2002 102 12 4581 4608 10.1021/cr0101757 12475202
14. Yeast aminopeptidase I Chemical composition and catalytic properties. Metz G, Rohm KH, Biochim Biophys Acta 1976 429 3 933 949 10.1016/0005-2744(76) 90338-7 5147
15. Tetrahedral aminopeptidase: a novel large protease complex from archaea. Franzetti B, Schoehn G, Hernandez JF, Jaquinod M, Ruigrok RW, Zaccai G, EMBO J 2002 21 9 2132 2138 10.1093/emboj/21.9.2132 11980710
16. Evolutionary families of metallopeptidases. Rawlings ND, Barrett AJ, Methods Enzymol 1995 248 183 228 7674922
17. Identification of histidine residues important in the catalysis and structure of aspartyl aminopeptidase. Wilk S, Wilk E, Magnusson RP, Arch Biochem Biophys 2002 407 2 176 183 10.1016/S0003-9861(02)00494-0 12413488
18. An archaeal peptidase assembles into two different quaternary structures: A tetrahedron and a giant octahedron. Schoehn G, Vellieux FM, Asuncion Dura M, Receveur-Brechot V, Fabry CM, Ruigrok RW, Ebel C, Roussel A, Franzetti B, J Biol Chem 2006 281 47 36327 36337 10.1074/jbc.M604417200 16973604
19. Crystal structure of a dodecameric tetrahedral-shaped aminopeptidase. Russo S, Baumann U, J Biol Chem 2004 279 49 51275 51281 10.1074/jbc.M409455200 15375159
20. Structural basis for the substrate specificity of PepA from Streptococcus pneumoniae, a dodecameric tetrahedral protease. Kim D, San BH, Moh SH, Park H, Kim DY, Lee S, Kim KK, Biochem Biophys Res Commun 2010 391 1 431 436 10.1016/j.bbrc.2009.11.075 19914209
21. Crystal structure of the dinuclear zinc aminopeptidase PepV from Lactobacillus delbrueckii unravels its preference for dipeptides. Jozic D, Bourenkow G, Bartunik H, Scholze H, Dive V, Henrich B, Huber R, Bode W, Maskos K, Structure 2002 10 8 1097 1106 10.1016/S0969-2126(02)00805-5 12176387
22. Crystal structure of carboxypeptidase G2, a bacterial enzyme with applications in cancer therapy. Rowsell S, Pauptit RA, Tucker AD, Melton RG, Blow DM, Brick P, Structure 1997 5 3 337 347 10.1016/S0969-2126(97)00191-3 9083113
23. Crystal structure of TET protease reveals complementary protein degradation pathways in prokaryotes. Borissenko L, Groll M, J Mol Biol 2005 346 5 1207 1219 10.1016/j.jmb.2004.12.056 15713475
24. The structural and biochemical characterizations of a novel TET peptidase complex from Pyrococcus horikoshii reveal an integrated peptide degradation system in hyperthermophilic Archaea. Dura MA, Rosenbaum E, Larabi A, Gabel F, Vellieux FM, Franzetti B, Mol Microbiol 2009 72 1 26 40 10.1111/j.1365-2958. 2009.06600.x 19291145
25. The CCP4 suite: programs for protein crystallography. CCP4, Acta Crystallogr D: Biol Crystallogr 1994 50 Pt 5 760 763
26. Likelihood-enhanced fast translation functions. McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ, Acta Crystallogr D: Biol Crystallogr 2005 61 Pt 4 458 464
27. Miscellaneous algorithms for density modification. Cowtan K, Main P, Acta crystallographica 1998 54 Pt 4 487 493
28. ARP/wARP and molecular replacement. Perrakis A, Harkiolaki M, Wilson KS, Lamzin VS, Acta crystallographica 2001 57 Pt 10 1445 1450
29. Refinement of macromolecular structures by the maximum-likelihood method. Murshudov GN, Vagin AA, Dodson EJ, Acta Crystallogr D: Biol Crystallogr 1997 53 Pt 3 240 255
30. Coot: model-building tools for molecular graphics. Emsley P, Cowtan K, Acta Crystallogr D: Biol Crystallogr 2004 60 Pt 12 2126 2132
31. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, Leith A, J Struct Biol 1996 116 1 190 199 10.1006/jsbi.1996.0030 8742743
32. Classification of macromolecular assemblies studied as 'single particles'. Frank J, Q Rev Biophys 1990 23 3 281 329 10.1017/S0033583500005564 2204955
33. Visualizing density maps with UCSF Chimera. Goddard TD, Huang CC, Ferrin TE, J Struct Biol 2007 157 1 281 287 10.1016/j.jsb.2006.06.010 16963278
34. Petrek M, Otyepka M, Banas P, Kosinova P, Koca J, Damborsky J, BMC Bioinformatics 2006 7 316 10.1186/1471-2105-7-316 16792811
35. Gilboa R, Greenblatt HM, Perach M, Spungin-Bialik A, Lessel U, Wohlfahrt G, Schomburg D, Blumberg S, Shoham G, Acta crystallographica 2000 56 Pt 5 551 558
36. Gilboa R, Spungin-Bialik A, Wohlfahrt G, Schomburg D, Blumberg S, Shoham G, Proteins 2001 44 4 490 504 10.1002/prot.1115 11484227
37. Chevrier B, D'Orchymont H, Schalk C, Tarnus C, Moras D, Eur J Biochem 1996 237 2 393 398 10.1111/j.1432-1033.1996.0393k.x 8647077