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PDBsum entry 1cp6
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protein ligands metals links
Hydrolase PDB id
1cp6

 

 

 

 

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Contents
Protein chain
291 a.a. *
Ligands
BUB
Metals
_ZN ×2
Waters ×136
* Residue conservation analysis
PDB id:
1cp6
Name: Hydrolase
Title: 1-butaneboronic acid binding to aeromonas proteolytica aminopeptidase
Structure: Protein (aminopeptidase). Chain: a. Ec: 3.4.11.10
Source: Vibrio proteolyticus. Organism_taxid: 671
Resolution:
1.90Å     R-factor:   0.193     R-free:   0.229
Authors: C.C.Depaola,B.Bennett,R.C.Holz,D.Ringe,G.A.Petsko
Key ref:
C.C.De Paola et al. (1999). 1-Butaneboronic acid binding to Aeromonas proteolytica aminopeptidase: a case of arrested development. Biochemistry, 38, 9048-9053. PubMed id: 10413478 DOI: 10.1021/bi9900572
Date:
08-Jun-99     Release date:   17-Jun-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Q01693  (AMPX_VIBPR) -  Bacterial leucyl aminopeptidase from Vibrio proteolyticus
Seq:
Struc: 		504 a.a.
291 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.11.10  - bacterial leucyl aminopeptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Release of an N-terminal amino acid, preferentially leucine, but not glutamic or aspartic acids.
      Cofactor: Zn(2+)

 

 
DOI no: 10.1021/bi9900572 Biochemistry 38:9048-9053 (1999)
PubMed id: 10413478  
 
 
1-Butaneboronic acid binding to Aeromonas proteolytica aminopeptidase: a case of arrested development.
C.C.De Paola, B.Bennett, R.C.Holz, D.Ringe, G.A.Petsko.
 
  ABSTRACT  
 
Hydrolases containing two metal ions connected by a bridging ligand catalyze reactions important in carcinogensis, tissue repair, post-translational modification, control and regulation of biochemical pathways, and protein degradation. The aminopeptidase from Aeromonas proteolytica serves as a paradigm for the study of such bridged bimetallic proteases since its three-dimensional structure is known to very high resolution and its catalytic reaction is amenable to spectroscopic examination. Herein, we report the X-ray crystal structure at 1.9 A resolution of AAP complexed with 1-butaneboronic acid (BuBA). This structure suggests that this complex represents a snapshot of the proteolytic reaction in an arrested form between the Michaelis complex and the transition state. Comparison of the structure with spectroscopic and other data allows us to conclude that the apparently structurally symmetrical dizinc site is actually asymmetric electrostatically.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20138056 B.P.Nocek, D.M.Gillner, Y.Fan, R.C.Holz, and A.Joachimiak (2010).
Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase.
  J Mol Biol, 397, 617-626.
PDB codes: 3ic1 3isz
18712420 D.M.Gillner, D.L.Bienvenue, B.P.Nocek, A.Joachimiak, V.Zachary, B.Bennett, and R.C.Holz (2009).
The dapE-encoded N-succinyl-L: ,L: -diaminopimelic acid desuccinylase from Haemophilus influenzae contains two active-site histidine residues.
  J Biol Inorg Chem, 14, 1.  
19233285 M.Hartley, and B.Bennett (2009).
Heterologous expression and purification of Vibrio proteolyticus (Aeromonas proteolytica) aminopeptidase: a rapid protocol.
  Protein Expr Purif, 66, 91.
PDB code: 3fh4
17608735 Y.F.Hershcovitz, R.Gilboa, V.Reiland, G.Shoham, and Y.Shoham (2007).
Catalytic mechanism of SGAP, a double-zinc aminopeptidase from Streptomyces griseus.
  FEBS J, 274, 3864-3876.  
16080009 J.Arima, Y.Uesugi, M.Iwabuchi, and T.Hatanaka (2006).
Study on peptide hydrolysis by aminopeptidases from Streptomyces griseus, Streptomyces septatus and Aeromonas proteolytica.
  Appl Microbiol Biotechnol, 70, 541-547.  
16751535 J.Arima, Y.Uesugi, M.Uraji, M.Iwabuchi, and T.Hatanaka (2006).
Dipeptide synthesis by an aminopeptidase from Streptomyces septatus TH-2 and its application to synthesis of biologically active peptides.
  Appl Environ Microbiol, 72, 4225-4231.  
16407307 J.Arima, Y.Uesugi, M.Uraji, S.Yatsushiro, S.Tsuboi, M.Iwabuchi, and T.Hatanaka (2006).
Modulation of Streptomyces leucine aminopeptidase by calcium: identification and functional analysis of key residues in activation and stabilization by calcium.
  J Biol Chem, 281, 5885-5894.  
16596389 W.Desmarais, D.L.Bienvenue, K.P.Bzymek, G.A.Petsko, D.Ringe, and R.C.Holz (2006).
The high-resolution structures of the neutral and the low pH crystals of aminopeptidase from Aeromonas proteolytica.
  J Biol Inorg Chem, 11, 398-408.
PDB codes: 1rtq 2dea
15138277 K.P.Bzymek, and R.C.Holz (2004).
The catalytic role of glutamate 151 in the leucine aminopeptidase from Aeromonas proteolytica.
  J Biol Chem, 279, 31018-31025.  
15375159 S.Russo, and U.Baumann (2004).
Crystal structure of a dodecameric tetrahedral-shaped aminopeptidase.
  J Biol Chem, 279, 51275-51281.
PDB code: 1xfo
14534321 S.Lundgren, Z.Gojković, J.Piskur, and D.Dobritzsch (2003).
Yeast beta-alanine synthase shares a structural scaffold and origin with dizinc-dependent exopeptidases.
  J Biol Chem, 278, 51851-51862.
PDB codes: 1r3n 1r43
12405829 B.Bennett, W.E.Antholine, V.M.D'souza, G.Chen, L.Ustinyuk, and R.C.Holz (2002).
Structurally distinct active sites in the copper(II)-substituted aminopeptidases from Aeromonas proteolytica and Escherichia coli.
  J Am Chem Soc, 124, 13025-13034.  
11258879 N.N.Kim, J.D.Cox, R.F.Baggio, F.A.Emig, S.K.Mistry, S.L.Harper, D.W.Speicher, S.M.Morris, D.E.Ash, A.Traish, and D.W.Christianson (2001).
Probing erectile function: S-(2-boronoethyl)-L-cysteine binds to arginase as a transition state analogue and enhances smooth muscle relaxation in human penile corpus cavernosum.
  Biochemistry, 40, 2678-2688.
PDB code: 1hq5
10736182 V.M.D'souza, B.Bennett, A.J.Copik, and R.C.Holz (2000).
Divalent metal binding properties of the methionyl aminopeptidase from Escherichia coli.
  Biochemistry, 39, 3817-3826.  
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.

 

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