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PDBsum entry 1azw

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protein Protein-protein interface(s) links
Aminopeptidase PDB id
1azw
Jmol
Contents
Protein chains
313 a.a. *
Waters ×199
* Residue conservation analysis
PDB id:
1azw
Name: Aminopeptidase
Title: Proline iminopeptidase from xanthomonas campestris pv. Citri
Structure: Proline iminopeptidase. Chain: a, b. Engineered: yes
Source: Xanthomonas citri. Organism_taxid: 346. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.70Å     R-factor:   0.192     R-free:   0.253
Authors: F.J.Medrano,J.Alonso,J.L.Garcia,A.Romero,W.Bode,F.X.Gomis- Ruth
Key ref:
F.J.Medrano et al. (1998). Structure of proline iminopeptidase from Xanthomonas campestris pv. citri: a prototype for the prolyl oligopeptidase family. EMBO J, 17, 1-9. PubMed id: 9427736 DOI: 10.1093/emboj/17.1.1
Date:
22-Nov-97     Release date:   13-Jan-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P52279  (PIP_XANCI) -  Proline iminopeptidase
Seq:
Struc:
313 a.a.
313 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.4.11.5  - Prolyl aminopeptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Release of a N-terminal proline from a peptide.
      Cofactor: Manganese
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     proteolysis   1 term 
  Biochemical function     hydrolase activity     3 terms  

 

 
DOI no: 10.1093/emboj/17.1.1 EMBO J 17:1-9 (1998)
PubMed id: 9427736  
 
 
Structure of proline iminopeptidase from Xanthomonas campestris pv. citri: a prototype for the prolyl oligopeptidase family.
F.J.Medrano, J.Alonso, J.L.García, A.Romero, W.Bode, F.X.Gomis-Rüth.
 
  ABSTRACT  
 
The proline iminopeptidase from Xanthomonas campestris pv. citri is a serine peptidase that catalyses the removal of N-terminal proline residues from peptides with high specificity. We have solved its three-dimensional structure by multiple isomorphous replacement and refined it to a crystallographic R-factor of 19.2% using X-ray data to 2.7 A resolution. The protein is folded into two contiguous domains. The larger domain shows the general topology of the alpha/beta hydrolase fold, with a central eight-stranded beta-sheet flanked by two helices and the 11 N-terminal residues on one side, and by four helices on the other side. The smaller domain is placed on top of the larger domain and essentially consists of six helices. The active site, located at the end of a deep pocket at the interface between both domains, includes a catalytic triad of Ser110, Asp266 and His294. Cys269, located at the bottom of the active site very close to the catalytic triad, presumably accounts for the inhibition by thiol-specific reagents. The overall topology of this iminopeptidase is very similar to that of yeast serine carboxypeptidase. The striking secondary structure similarity to human lymphocytic prolyl oligopeptidase and dipeptidyl peptidase IV makes this proline iminopeptidase structure a suitable model for the three-dimensional structure of other peptidases of this family.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 Solid surface stereo representation of the electrostatic potential of the proline iminopeptidase monomer. The colour coding is according to the surface potential from negative (red) to positive (blue). The view is down the active site funnel, at the interface between the lower and the upper domain. The positive charge of the histidine of the catalytic triad is clearly visible in the middle of the active site. This figure was prepared with GRASP (Nicholls et al., 1993).
Figure 5.
Figure 5 Stereo view of the active site showing the catalytic triad residues (Ser110, Asp266 and His294), Glu201 and Glu230, probably involved in the binding of the amino-terminal group of the substrate, Arg133, located in the putative S1' position, Trp111, Gly42 and Gly43, shaping the oxyanion-binding site, and the solvent molecule, Sol584, in close contact with the two glutamates and the catalytic serine. This figure was prepared with TURBO-FRODO (Roussel and Cambilleau, 1992).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1998, 17, 1-9) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20444688 M.Li, C.Chen, D.R.Davies, and T.K.Chiu (2010).
Induced-fit mechanism for prolyl endopeptidase.
  J Biol Chem, 285, 21487-21495.
PDB codes: 3iuj 3iul 3ium 3iun 3iuq 3iur 3ivm
20078865 M.Liu, J.R.Bayjanov, B.Renckens, A.Nauta, and R.J.Siezen (2010).
The proteolytic system of lactic acid bacteria revisited: a genomic comparison.
  BMC Genomics, 11, 36.  
19088317 A.V.Patankar, and J.E.González (2009).
An orphan LuxR homolog of Sinorhizobium meliloti affects stress adaptation and competition for nodulation.
  Appl Environ Microbiol, 75, 946-955.  
19556294 C.S.Mahon, A.J.O'Donoghue, D.H.Goetz, P.G.Murray, C.S.Craik, and M.G.Tuohy (2009).
Characterization of a multimeric, eukaryotic prolyl aminopeptidase: an inducible and highly specific intracellular peptidase from the non-pathogenic fungus Talaromyces emersonii.
  Microbiology, 155, 3673-3682.  
18175319 M.Okai, Y.Miyauchi, A.Ebihara, W.C.Lee, K.Nagata, and M.Tanokura (2008).
Crystal structure of the proline iminopeptidase-related protein TTHA1809 from Thermus thermophilus HB8.
  Proteins, 70, 1646-1649.
PDB code: 2yys
17318535 B.Geueke, and H.P.Kohler (2007).
Bacterial beta-peptidyl aminopeptidases: on the hydrolytic degradation of beta-peptides.
  Appl Microbiol Biotechnol, 74, 1197-1204.  
17581124 L.Zhang, Y.Jia, L.Wang, and R.Fang (2007).
A proline iminopeptidase gene upregulated in planta by a LuxR homologue is essential for pathogenicity of Xanthomonas campestris pv. campestris.
  Mol Microbiol, 65, 121-136.  
  16754966 C.Y.Yang, K.H.Chin, C.C.Chou, A.H.Wang, and S.H.Chou (2006).
Structure of XC6422 from Xanthomonas campestris at 1.6 A resolution: a small serine alpha/beta-hydrolase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 498-503.
PDB code: 2fuk
15654623 D.E.Basten, A.P.Moers, A.J.Ooyen, and P.J.Schaap (2005).
Characterisation of Aspergillus niger prolyl aminopeptidase.
  Mol Genet Genomics, 272, 673-679.  
15994304 P.Goettig, H.Brandstetter, M.Groll, W.Göhring, P.V.Konarev, D.I.Svergun, R.Huber, and J.S.Kim (2005).
X-ray snapshots of peptide processing in mutants of tricorn-interacting factor F1 from Thermoplasma acidophilum.
  J Biol Chem, 280, 33387-33396.
PDB codes: 1xqv 1xqw 1xqx 1xqy 1xrl 1xrm 1xrn 1xro 1xrp 1xrq 1xrr
15819895 P.Rigolet, X.G.Xi, S.Rety, and J.F.Chich (2005).
The structural comparison of the bacterial PepX and human DPP-IV reveals sites for the design of inhibitors of PepX activity.
  FEBS J, 272, 2050-2059.  
15066172 H.Komeda, H.Harada, S.Washika, T.Sakamoto, M.Ueda, and Y.Asano (2004).
S-stereoselective piperazine-2-tert-butylcarboxamide hydrolase from Pseudomonas azotoformans IAM 1603 is a novel L-amino acid amidase.
  Eur J Biochem, 271, 1465-1475.  
12511496 I.Nagy, T.Banerjee, T.Tamura, G.Schoofs, A.Gils, P.Proost, N.Tamura, W.Baumeister, and R.De Mot (2003).
Characterization of a novel intracellular endopeptidase of the alpha/beta hydrolase family from Streptomyces coelicolor A3(2).
  J Bacteriol, 185, 496-503.  
12690074 M.Engel, T.Hoffmann, L.Wagner, M.Wermann, U.Heiser, R.Kiefersauer, R.Huber, W.Bode, H.U.Demuth, and H.Brandstetter (2003).
The crystal structure of dipeptidyl peptidase IV (CD26) reveals its functional regulation and enzymatic mechanism.
  Proc Natl Acad Sci U S A, 100, 5063-5068.
PDB codes: 1orv 1orw
12111749 C.T.Supuran, A.Scozzafava, and B.W.Clare (2002).
Bacterial protease inhibitors.
  Med Res Rev, 22, 329-372.  
11933063 E.Shaw, L.A.McCue, C.E.Lawrence, and J.S.Dordick (2002).
Identification of a novel class in the alpha/beta hydrolase fold superfamily: the N-myc differentiation-related proteins.
  Proteins, 47, 163-168.  
12011065 J.J.Polderman-Tijmes, P.A.Jekel, C.M.Jeronimus-Stratingh, A.P.Bruins, J.M.Van Der Laan, T.Sonke, and D.B.Janssen (2002).
Identification of the catalytic residues of alpha-amino acid ester hydrolase from Acetobacter turbidans by labeling and site-directed mutagenesis.
  J Biol Chem, 277, 28474-28482.  
11796618 J.M.Goldstein, D.Nelson, T.Kordula, J.A.Mayo, and J.Travis (2002).
Extracellular arginine aminopeptidase from Streptococcus gordonii FSS2.
  Infect Immun, 70, 836-843.  
12454479 M.M.Mehanni, A.P.Turnbull, S.E.Sedelnikova, P.J.Baker, S.Foster, and D.W.Rice (2002).
Crystallization and preliminary X-ray analysis of the ytxM gene product from Bacillus subtilis.
  Acta Crystallogr D Biol Crystallogr, 58, 2138-2140.  
12374735 P.Goettig, M.Groll, J.S.Kim, R.Huber, and H.Brandstetter (2002).
Structures of the tricorn-interacting aminopeptidase F1 with different ligands explain its catalytic mechanism.
  EMBO J, 21, 5343-5352.
PDB codes: 1mt3 1mtz 1mu0
10673442 C.Bompard-Gilles, V.Villeret, G.J.Davies, L.Fanuel, B.Joris, J.M.Frère, and J.Van Beeumen (2000).
A new variant of the Ntn hydrolase fold revealed by the crystal structure of L-aminopeptidase D-ala-esterase/amidase from Ochrobactrum anthropi.
  Structure, 8, 153-162.
PDB code: 1b65
10673439 J.Zou, B.M.Hallberg, T.Bergfors, F.Oesch, M.Arand, S.L.Mowbray, and T.A.Jones (2000).
Structure of Aspergillus niger epoxide hydrolase at 1.8 A resolution: implications for the structure and function of the mammalian microsomal class of epoxide hydrolases.
  Structure, 8, 111-122.
PDB code: 1qo7
11106384 K.Håkansson, A.H.Wang, and C.G.Miller (2000).
The structure of aspartyl dipeptidase reveals a unique fold with a Ser-His-Glu catalytic triad.
  Proc Natl Acad Sci U S A, 97, 14097-14102.
PDB codes: 1fy2 1fye
  10338021 B.Zhang, L.Rychlewski, K.Paw┼éowski, J.S.Fetrow, J.Skolnick, and A.Godzik (1999).
From fold predictions to function predictions: automation of functional site conservation analysis for functional genome predictions.
  Protein Sci, 8, 1104-1115.  
10583373 C.A.Abbott, G.W.McCaughan, M.T.Levy, W.B.Church, and M.D.Gorrell (1999).
Binding to human dipeptidyl peptidase IV by adenosine deaminase and antibodies that inhibit ligand binding involves overlapping, discontinuous sites on a predicted beta propeller domain.
  Eur J Biochem, 266, 798-810.  
10545093 F.X.Gomis-Rüth, V.Companys, Y.Qian, L.D.Fricker, J.Vendrell, F.X.Avilés, and M.Coll (1999).
Crystal structure of avian carboxypeptidase D domain II: a prototype for the regulatory metallocarboxypeptidase subfamily.
  EMBO J, 18, 5817-5826.
PDB code: 1qmu
10187837 K.Redding, L.Cournac, I.R.Vassiliev, J.H.Golbeck, G.Peltier, and J.D.Rochaix (1999).
Photosystem I is indispensable for photoautotrophic growth, CO2 fixation, and H2 photoproduction in Chlamydomonas reinhardtii.
  J Biol Chem, 274, 10466-10473.  
9700512 J.Wang, and T.A.Springer (1998).
Structural specializations of immunoglobulin superfamily members for adhesion to integrins and viruses.
  Immunol Rev, 163, 197-215.  
9845366 N.Tamura, F.Lottspeich, W.Baumeister, and T.Tamura (1998).
The role of tricorn protease and its aminopeptidase-interacting factors in cellular protein degradation.
  Cell, 95, 637-648.  
9695945 V.Fülöp, Z.Böcskei, and L.Polgár (1998).
Prolyl oligopeptidase: an unusual beta-propeller domain regulates proteolysis.
  Cell, 94, 161-170.
PDB codes: 1qfm 1qfs
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 codes are shown on the right.