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PDBsum entry 1bqb

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protein metals links
Hydrolase PDB id
1bqb
Jmol
Contents
Protein chain
301 a.a. *
Metals
_CA ×3
_ZN
Waters ×160
* Residue conservation analysis
PDB id:
1bqb
Name: Hydrolase
Title: Aureolysin, staphylococcus aureus metalloproteinase
Structure: Protein (aureolysin). Chain: a. Synonym: staphylococcus aureus metalloproteinase. Ec: 3.4.24.27
Source: Staphylococcus aureus. Organism_taxid: 1280. Strain: v8-bc10
Resolution:
1.72Å     R-factor:   0.176     R-free:   0.239
Authors: F.J.Medrano,A.Banbula,J.Potempa,J.Travis,W.Bode
Key ref:
A.Banbula et al. (1998). Amino-acid sequence and three-dimensional structure of the Staphylococcus aureus metalloproteinase at 1.72 A resolution. Structure, 6, 1185-1193. PubMed id: 9753696 DOI: 10.1016/S0969-2126(98)00118-X
Date:
14-Jul-98     Release date:   13-Jan-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P81177  (AURE_STAAU) -  Zinc metalloproteinase aureolysin
Seq:
Struc:
509 a.a.
301 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     metalloendopeptidase activity     1 term  

 

 
DOI no: 10.1016/S0969-2126(98)00118-X Structure 6:1185-1193 (1998)
PubMed id: 9753696  
 
 
Amino-acid sequence and three-dimensional structure of the Staphylococcus aureus metalloproteinase at 1.72 A resolution.
A.Banbula, J.Potempa, J.Travis, C.Fernandez-Catalán, K.Mann, R.Huber, W.Bode, F.Medrano.
 
  ABSTRACT  
 
BACKGROUND: Aureolysin is an extracellular zinc-dependent metalloproteinase from the pathogenic bacterium Staphylococcus aureus. This enzyme exhibits in vitro activity against several molecules of biological significance for the host, indicating that it is involved in the pathology of staphylococcal diseases. RESULTS: Here we report the amino-acid sequence and inhibitor-free X-ray crystal structure of aureolysin, a member of the thermolysin family of zinc-dependent metalloproteinases. This enzyme, which binds one zinc and three calcium ions, comprises a single chain of 301 amino acids that consists of a beta-strand-rich upper domain and an alpha-helix-rich lower domain. CONCLUSIONS: The overall structure of aureolysin is very similar to that of the other three members of this family whose structures are known - thermolysin (TLN) from Bacillus thermoproteolyticus, neutral protease (NP) from Bacillus cereus and elastase (PAE) from Pseudomonas aeruginosa. But an important difference has been encountered: in contrast to what has been observed in the other three members of this family (TLN, NP and PAE), inhibitor-free aureolysin displays a 'closed' active site cleft conformation. This new structure therefore raises questions about the universality of the hinge-bending motion model for the neutral metalloproteinases.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Superposition of (a) the residues from the N-terminal subdomain that contribute to the `upper' lip of the active-site cleft and (b) the calcium-binding sites of aureolysin on thermolysin. The spheres represent the calcium ions. Aureolysin is shown in black and thermolysin in grey. This figure was prepared with the program SETOR [34].
 
  The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 1185-1193) copyright 1998.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23275160 A.Ruf, M.Stihle, J.Benz, M.Schmidt, and H.Sobek (2013).
Structure of Gentlyase, the neutral metalloprotease of Paenibacillus polymyxa.
  Acta Crystallogr D Biol Crystallogr, 69, 24-31.
PDB codes: 4b52 4ger
19915005 I.V.Demidyuk, T.Y.Gromova, K.M.Polyakov, W.R.Melik-Adamyan, I.P.Kuranova, and S.V.Kostrov (2010).
Crystal structure of the protealysin precursor: insights into propeptide function.
  J Biol Chem, 285, 2003-2013.
PDB code: 2vqx
20337595 N.Beaufort, P.Seweryn, S.de Bentzmann, A.Tang, J.Kellermann, N.Grebenchtchikov, M.Schmitt, C.P.Sommerhoff, D.Pidard, and V.Magdolen (2010).
Activation of human pro-urokinase by unrelated proteases secreted by Pseudomonas aeruginosa.
  Biochem J, 428, 473-482.  
19181663 B.B.Xie, F.Bian, X.L.Chen, H.L.He, J.Guo, X.Gao, Y.X.Zeng, B.Chen, B.C.Zhou, and Y.Z.Zhang (2009).
Cold adaptation of zinc metalloproteases in the thermolysin family from deep sea and arctic sea ice bacteria revealed by catalytic and structural properties and molecular dynamics: new insights into relationship between conformational flexibility and hydrogen bonding.
  J Biol Chem, 284, 9257-9269.  
19152630 O.A.Adekoya, and I.Sylte (2009).
The thermolysin family (m4) of enzymes: therapeutic and biotechnological potential.
  Chem Biol Drug Des, 73, 7.  
18664262 A.J.Sabat, B.Wladyka, K.Kosowska-Shick, H.Grundmann, J.M.van Dijl, J.Kowal, P.C.Appelbaum, A.Dubin, and W.Hryniewicz (2008).
Polymorphism, genetic exchange and intragenic recombination of the aureolysin gene among Staphylococcus aureus strains.
  BMC Microbiol, 8, 129.  
17965168 A.P.Bitar, M.Cao, and H.Marquis (2008).
The metalloprotease of Listeria monocytogenes is activated by intramolecular autocatalysis.
  J Bacteriol, 190, 107-111.  
17878159 N.N.Nickerson, L.Prasad, L.Jacob, L.T.Delbaere, and M.J.McGavin (2007).
Activation of the SspA serine protease zymogen of Staphylococcus aureus proceeds through unique variations of a trypsinogen-like mechanism and is dependent on both autocatalytic and metalloprotease-specific processing.
  J Biol Chem, 282, 34129-34138.  
16390957 F.C.Tenover, L.K.McDougal, R.V.Goering, G.Killgore, S.J.Projan, J.B.Patel, and P.M.Dunman (2006).
Characterization of a strain of community-associated methicillin-resistant Staphylococcus aureus widely disseminated in the United States.
  J Clin Microbiol, 44, 108-118.  
15601711 M.Kawalec, J.Potempa, J.L.Moon, J.Travis, and B.E.Murray (2005).
Molecular diversity of a putative virulence factor: purification and characterization of isoforms of an extracellular serine glutamyl endopeptidase of Enterococcus faecalis with different enzymatic activities.
  J Bacteriol, 187, 266-275.  
11859085 A.de Kreij, B.van den Burg, G.Venema, G.Vriend, V.G.Eijsink, and J.E.Nielsen (2002).
The effects of modifying the surface charge on the catalytic activity of a thermolysin-like protease.
  J Biol Chem, 277, 15432-15438.  
12111749 C.T.Supuran, A.Scozzafava, and B.W.Clare (2002).
Bacterial protease inhibitors.
  Med Res Rev, 22, 329-372.  
12437090 G.Dubin (2002).
Extracellular proteases of Staphylococcus spp.
  Biol Chem, 383, 1075-1086.  
11559368 A.de Kreij, B.van den Burg, O.R.Veltman, G.Vriend, G.Venema, and V.G.Eijsink (2001).
The effect of changing the hydrophobic S1' subsite of thermolysin-like proteases on substrate specificity.
  Eur J Biochem, 268, 4985-4991.  
11767947 G.Dubin, D.Chmiel, P.Mak, M.Rakwalska, M.Rzychon, and A.Dubin (2001).
Molecular cloning and biochemical characterisation of proteases from Staphylococcus epidermidis.
  Biol Chem, 382, 1575-1582.  
11223512 T.Hori, T.Kumasaka, M.Yamamoto, N.Nonaka, N.Tanaka, Y.Hashimoto, U.Ueki, and K.Takio (2001).
Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms.
  Acta Crystallogr D Biol Crystallogr, 57, 361-368.
PDB codes: 1g12 1ge5 1ge6 1ge7
10639475 A.Sabat, K.Kosowska, K.Poulsen, A.Kasprowicz, A.Sekowska, B.van Den Burg, J.Travis, and J.Potempa (2000).
Two allelic forms of the aureolysin gene (aur) within Staphylococcus aureus.
  Infect Immun, 68, 973-976.  
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.