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PDBsum entry 2dqm

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protein ligands metals links
Hydrolase PDB id
2dqm
Jmol
Contents
Protein chain
867 a.a. *
Ligands
SO4 ×2
BES
Metals
_ZN
Waters ×946
* Residue conservation analysis
PDB id:
2dqm
Name: Hydrolase
Title: Crystal structure of aminopeptidase n complexed with bestatin
Structure: Aminopeptidase n. Chain: a. Synonym: alpha-aminoacylpeptide hydrolase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: pepn. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.60Å     R-factor:   0.182     R-free:   0.194
Authors: Y.Onohara,Y.Nakajima,K.Ito,T.Yoshimoto
Key ref:
K.Ito et al. (2006). Crystal structure of aminopeptidase N (proteobacteria alanyl aminopeptidase) from Escherichia coli and conformational change of methionine 260 involved in substrate recognition. J Biol Chem, 281, 33664-33676. PubMed id: 16885166 DOI: 10.1074/jbc.M605203200
Date:
29-May-06     Release date:   01-Aug-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04825  (AMPN_ECOLI) -  Aminopeptidase N
Seq:
Struc:
 
Seq:
Struc:
870 a.a.
867 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.11.2  - Membrane alanyl aminopeptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Release of an N-terminal amino acid, Xaa-|-Xbb- from a peptide, amide or arylamide. Xaa is preferably Ala, but may be most amino acids including Pro (slow action). When a terminal hydrophobic residue is followed by a prolyl residue, the two may be released as an intact Xaa-Pro dipeptide.
      Cofactor: Zn(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     peptide catabolic process   2 terms 
  Biochemical function     hydrolase activity     7 terms  

 

 
DOI no: 10.1074/jbc.M605203200 J Biol Chem 281:33664-33676 (2006)
PubMed id: 16885166  
 
 
Crystal structure of aminopeptidase N (proteobacteria alanyl aminopeptidase) from Escherichia coli and conformational change of methionine 260 involved in substrate recognition.
K.Ito, Y.Nakajima, Y.Onohara, M.Takeo, K.Nakashima, F.Matsubara, T.Ito, T.Yoshimoto.
 
  ABSTRACT  
 
Aminopeptidase N from Escherichia coli is a broad specificity zinc exopeptidase belonging to aminopeptidase clan MA, family M1. The structures of the ligand-free form and the enzyme-bestatin complex were determined at 1.5- and 1.6-A resolution, respectively. The enzyme is composed of four domains: an N-terminal beta-domain (Met(1)-Asp(193)), a catalytic domain (Phe(194)-Gly(444)), a middle beta-domain (Thr(445)-Trp(546)), and a C-terminal alpha-domain (Ser(547)-Ala(870)). The structure of the catalytic domain exhibits similarity to thermolysin, and a metal-binding motif (HEXXHX(18)E) is found in the domain. The zinc ion is coordinated by His(297), His(301), Glu(320), and a water molecule. The groove on the catalytic domain that contains the active site is covered by the C-terminal alpha-domain, and a large cavity is formed inside the protein. However, there exists a small hole at the center of the C-terminal alpha-domain. The N terminus of bestatin is recognized by Glu(121) and Glu(264), which are located in the N-terminal and catalytic domains, respectively. Glu(298) and Tyr(381), located near the zinc ion, are considered to be involved in peptide cleavage. A difference revealed between the ligand-free form and the enzyme-bestatin complex indicated that Met(260) functions as a cushion to accept substrates with different N-terminal residue sizes, resulting in the broad substrate specificity of this enzyme.
 
  Selected figure(s)  
 
Figure 6.
FIGURE 6. Protein surface stereo diagrams of peptidase family M1 enzymes. a, aminopeptidase N; b, human leukotriene A[4] hydrolase (Protein Data Bank code 1HS6); c, T. acidophilum tricorn-interacting factor F3 (Protein Data Bank code 1Z1W). The three enzymes are indicated in the respective colors used to represent corresponding regions based on the domains of aminopeptidase N, i.e. N-terminal -domain (blue), catalytic domain (cyan), middle -domain (green), and C-terminal -domain (pink). The arrows indicate the expected sites for the entry of substrates into the active site of the three enzymes.
Figure 8.
FIGURE 8. Catalytic mechanism of aminopeptidase N. a, free enzyme; b, Michaelis complex; c, tetrahedral intermediate; d, enzyme complexed with an amino acid product.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 33664-33676) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21493078 J.Su, Q.Wang, J.Feng, C.Zhang, D.Zhu, T.Wei, W.Xu, and L.Gu (2011).
Engineered Thermoplasma acidophilum factor F3 mimics human aminopeptidase N (APN) as a target for anticancer drug development.
  Bioorg Med Chem, 19, 2991-2996.
PDB code: 3q7j
20676100 C.K.Chuang, B.Rockel, G.Seyit, P.J.Walian, A.M.Schönegge, J.Peters, P.H.Zwart, W.Baumeister, and B.K.Jap (2010).
Hybrid molecular structure of the giant protease tripeptidyl peptidase II.
  Nat Struct Mol Biol, 17, 990-996.
PDB code: 3lxu
21150094 E.Menach, K.Yasukawa, and K.Inouye (2010).
Effects of site-directed mutagenesis of the loop residue of the N-terminal domain Gly117 of thermolysin on its catalytic activity.
  Biosci Biotechnol Biochem, 74, 2457-2462.  
20706583 S.Vaiyapuri, S.C.Wagstaff, K.A.Watson, R.A.Harrison, J.M.Gibbins, and E.G.Hutchinson (2010).
Purification and functional characterisation of rhiminopeptidase A, a novel aminopeptidase from the venom of Bitis gabonica rhinoceros.
  PLoS Negl Trop Dis, 4, e796.  
  19707293 A.Singh, and C.Sivaprasad (2009).
Functional interpretation of APN receptor from M.sexta using a molecular model.
  Bioinformation, 3, 321-325.  
19228697 C.Claperon, I.Banegas-Font, X.Iturrioz, R.Rozenfeld, B.Maigret, and C.Llorens-Cortes (2009).
Identification of threonine 348 as a residue involved in aminopeptidase A substrate specificity.
  J Biol Chem, 284, 10618-10626.  
19622865 M.C.Fournié-Zaluski, H.Poras, B.P.Roques, Y.Nakajima, K.Ito, and T.Yoshimoto (2009).
Structure of aminopeptidase N from Escherichia coli complexed with the transition-state analogue aminophosphinic inhibitor PL250.
  Acta Crystallogr D Biol Crystallogr, 65, 814-822.
PDB code: 2zxg
19819873 M.Maruyama, N.Arisaka, Y.Goto, Y.Ohsawa, H.Inoue, H.Fujiwara, A.Hattori, and M.Tsujimoto (2009).
Histidine 379 of human laeverin/aminopeptidase Q, a nonconserved residue within the exopeptidase motif, defines its distinctive enzymatic properties.
  J Biol Chem, 284, 34692-34702.  
19683842 Q.Li, H.Fang, X.Wang, L.Hu, and W.Xu (2009).
Novel cyclic-imide peptidomimetics as aminopeptidase N inhibitors. Design, chemistry and activity evaluation. Part I.
  Eur J Med Chem, 44, 4819-4825.  
19196988 S.McGowan, C.J.Porter, J.Lowther, C.M.Stack, S.J.Golding, T.S.Skinner-Adams, K.R.Trenholme, F.Teuscher, S.M.Donnelly, J.Grembecka, A.Mucha, P.Kafarski, R.Degori, A.M.Buckle, D.L.Gardiner, J.C.Whisstock, and J.P.Dalton (2009).
Structural basis for the inhibition of the essential Plasmodium falciparum M1 neutral aminopeptidase.
  Proc Natl Acad Sci U S A, 106, 2537-2542.
PDB codes: 3ebg 3ebh 3ebi
18163885 B.Salopek-Sondi, B.Vukelić, J.Spoljarić, S.Simaga, D.Vujaklija, J.Makarević, N.Jajcanin, and M.Abramić (2008).
Functional tyrosine residue in the active center of human dipeptidyl peptidase III.
  Biol Chem, 389, 163-167.  
18523486 S.Ye, S.Y.Chai, R.A.Lew, D.B.Ascher, C.J.Morton, M.W.Parker, and A.L.Albiston (2008).
Identification of modulating residues defining the catalytic cleft of insulin-regulated aminopeptidase.
  Biochem Cell Biol, 86, 251-261.  
19018282 T.Zhou, P.J.Enyeart, and C.O.Wilke (2008).
Detecting clusters of mutations.
  PLoS ONE, 3, e3765.  
18820015 Y.Nakajima, K.Ito, T.Toshima, T.Egawa, H.Zheng, H.Oyama, Y.F.Wu, E.Takahashi, K.Kyono, and T.Yoshimoto (2008).
Dipeptidyl aminopeptidase IV from Stenotrophomonas maltophilia exhibits activity against a substrate containing a 4-hydroxyproline residue.
  J Bacteriol, 190, 7819-7829.
PDB code: 2ecf
17603262 T.Yoshimoto (2007).
[Biochemistry and structural biology of microbial enzymes and their medical applications]
  Yakugaku Zasshi, 127, 1035-1045.  
17974014 V.L.Pham, M.S.Cadel, C.Gouzy-Darmon, C.Hanquez, M.C.Beinfeld, P.Nicolas, C.Etchebest, and T.Foulon (2007).
Aminopeptidase B, a glucagon-processing enzyme: site directed mutagenesis of the Zn2+-binding motif and molecular modelling.
  BMC Biochem, 8, 21.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.