PDBsum entry 1npc

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Hydrolase(metalloproteinase) PDB id
Protein chain
317 a.a. *
_CA ×4
Waters ×304
* Residue conservation analysis
PDB id:
Name: Hydrolase(metalloproteinase)
Title: The structure of neutral protease from bacillus cereus at 0.2-nm resolution
Structure: Neutral protease. Chain: a. Engineered: yes
Source: Bacillus cereus. Organism_taxid: 1396
2.00Å     R-factor:   0.175    
Authors: W.Stark,R.A.Pauptit,J.N.Jansonius
Key ref: W.Stark et al. (1992). The structure of neutral protease from Bacillus cereus at 0.2-nm resolution. Eur J Biochem, 207, 781-791. PubMed id: 1633827
08-Jan-92     Release date:   31-Oct-93    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P05806  (NPRE_BACCE) -  Bacillolysin
566 a.a.
317 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Bacillolysin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Similar, but not identical, to that of thermolysin.
      Cofactor: Calcium; Zinc
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     metalloendopeptidase activity     1 term  


Eur J Biochem 207:781-791 (1992)
PubMed id: 1633827  
The structure of neutral protease from Bacillus cereus at 0.2-nm resolution.
W.Stark, R.A.Pauptit, K.S.Wilson, J.N.Jansonius.
The crystal structure of the neutral protease from Bacillus cereus has been refined to an R factor of 17.5% at 0.2-nm resolution. The enzyme, an extracellular metalloendopeptidase, consists of two domains and binds one zinc and four calcium ions. The structure is very similar to that of thermolysin, with which the enzyme shares 73% amino-acid sequence identity. The active-site cleft between the two domains is wider in neutral protease than in thermolysin. This suggests the presence of a flexible hinge region between the two domains, which may assist enzyme action. The high-resolution analysis allows detailed examination of possible causes for the difference in thermostability between neutral protease and thermolysin.

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
21153672 D.Chakravorty, S.Parameswaran, V.K.Dubey, and S.Patra (2011).
In silico characterization of thermostable lipases.
  Extremophiles, 15, 89.  
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
19152630 O.A.Adekoya, and I.Sylte (2009).
The thermolysin family (m4) of enzymes: therapeutic and biotechnological potential.
  Chem Biol Drug Des, 73, 7.  
17828423 P.C.Bruijnincx, M.Lutz, J.P.den Breejen, A.L.Spek, G.van Koten, and R.J.Klein Gebbink (2007).
Zinc complexes of the biomimetic N,N,O ligand family of substituted 3,3-bis(1-alkylimidazol-2-yl)propionates: the formation of oxalate from pyruvate.
  J Biol Inorg Chem, 12, 1181-1196.  
16617426 H.Deng, G.Chen, W.Yang, and J.J.Yang (2006).
Predicting calcium-binding sites in proteins - a graph theory and geometry approach.
  Proteins, 64, 34-42.  
15843974 B.Ghorbel-Frikha, A.Sellami-Kamoun, N.Fakhfakh, A.Haddar, L.Manni, and M.Nasri (2005).
Production and purification of a calcium-dependent protease from Bacillus cereus BG1.
  J Ind Microbiol Biotechnol, 32, 186-194.  
12517141 A.Saghatelian, K.M.Guckian, D.A.Thayer, and M.R.Ghadiri (2003).
DNA detection and signal amplification via an engineered allosteric enzyme.
  J Am Chem Soc, 125, 344-345.  
12037302 A.C.Hausrath, and B.W.Matthews (2002).
Thermolysin in the absence of substrate has an open conformation.
  Acta Crystallogr D Biol Crystallogr, 58, 1002-1007.
PDB code: 1l3f
12011042 H.Tsukada, and T.Pourmotabbed (2002).
Unexpected crucial role of residue 272 in substrate specificity of fibroblast collagenase.
  J Biol Chem, 277, 27378-27384.  
11087953 N.Panasik, J.E.Brenchley, and G.K.Farber (2000).
Distributions of structural features contributing to thermostability in mesophilic and thermophilic alpha/beta barrel glycosyl hydrolases.
  Biochim Biophys Acta, 1543, 189-201.  
10347149 P.M.Cummins, A.Pabon, E.H.Margulies, and M.J.Glucksman (1999).
Zinc coordination and substrate catalysis within the neuropeptide processing enzyme endopeptidase EC Identification of active site histidine and glutamate residues.
  J Biol Chem, 274, 16003-16009.  
9753696 A.Banbula, J.Potempa, J.Travis, C.Fernandez-Catalán, K.Mann, R.Huber, W.Bode, and F.Medrano (1998).
Amino-acid sequence and three-dimensional structure of the Staphylococcus aureus metalloproteinase at 1.72 A resolution.
  Structure, 6, 1185-1193.
PDB code: 1bqb
  10082367 I.L.Alberts, K.Nadassy, and S.J.Wodak (1998).
Analysis of zinc binding sites in protein crystal structures.
  Protein Sci, 7, 1700-1716.  
9548763 O.R.Veltman, G.Vriend, H.J.Berendsen, B.Van den Burg, G.Venema, and V.G.Eijsink (1998).
A single calcium binding site is crucial for the calcium-dependent thermal stability of thermolysin-like proteases.
  Biochemistry, 37, 5312-5319.  
9548762 O.R.Veltman, V.G.Eijsink, G.Vriend, Kreij, G.Venema, and B.Van den Burg (1998).
Probing catalytic hinge bending motions in thermolysin-like proteases by glycine --> alanine mutations.
  Biochemistry, 37, 5305-5311.  
9720222 S.Kojima, T.Kumazaki, S.Ishii, and K.Miura (1998).
Primary structure of Streptomyces griseus metalloendopeptidase II.
  Biosci Biotechnol Biochem, 62, 1392-1398.  
9111013 J.Mansfeld, G.Vriend, B.W.Dijkstra, O.R.Veltman, B.Van den Burg, G.Venema, R.Ulbrich-Hofmann, and V.G.Eijsink (1997).
Extreme stabilization of a thermolysin-like protease by an engineered disulfide bond.
  J Biol Chem, 272, 11152-11156.  
9346299 O.R.Veltman, G.Vriend, F.Hardy, J.Mansfeld, B.van den Burg, G.Venema, and V.G.Eijsink (1997).
Mutational analysis of a surface area that is critical for the thermal stability of thermolysin-like proteases.
  Eur J Biochem, 248, 433-440.  
8900115 M.J.O'Donohue, and A.Beaumont (1996).
The roles of the prosequence of thermolysin in enzyme inhibition and folding in vitro.
  J Biol Chem, 271, 26477-26481.  
7675786 D.M.van Aalten, A.Amadei, A.B.Linssen, V.G.Eijsink, G.Vriend, and H.J.Berendsen (1995).
The essential dynamics of thermolysin: confirmation of the hinge-bending motion and comparison of simulations in vacuum and water.
  Proteins, 22, 45-54.  
  8535232 D.R.Holland, A.C.Hausrath, D.Juers, and B.W.Matthews (1995).
Structural analysis of zinc substitutions in the active site of thermolysin.
  Protein Sci, 4, 1955-1965.
PDB codes: 1lna 1lnb 1lnc 1lnd 1lne 1lnf
7762303 H.Voss, J.Tamames, C.Teodoru, A.Valencia, C.Sensen, S.Wiemann, C.Schwager, J.Zimmermann, C.Sander, and W.Ansorge (1995).
Nucleotide sequence and analysis of the centromeric region of yeast chromosome IX.
  Yeast, 11, 61-78.  
8591026 K.S.Yip, T.J.Stillman, K.L.Britton, P.J.Artymiuk, P.J.Baker, S.E.Sedelnikova, P.C.Engel, A.Pasquo, R.Chiaraluce, and V.Consalvi (1995).
The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures.
  Structure, 3, 1147-1158.
PDB codes: 1gtm 1hrd
8747456 M.Hennig, B.Darimont, R.Sterner, K.Kirschner, and J.N.Jansonius (1995).
2.0 A structure of indole-3-glycerol phosphate synthase from the hyperthermophile Sulfolobus solfataricus: possible determinants of protein stability.
  Structure, 3, 1295-1306.
PDB code: 1igs
7664094 V.G.Eijsink, O.R.Veltman, W.Aukema, G.Vriend, and G.Venema (1995).
Structural determinants of the stability of thermolysin-like proteinases.
  Nat Struct Biol, 2, 374-379.  
8143751 B.Van den Burg, B.W.Dijkstra, G.Vriend, B.Van der Vinne, G.Venema, and V.G.Eijsink (1994).
Protein stabilization by hydrophobic interactions at the surface.
  Eur J Biochem, 220, 981-985.  
  8302217 C.C.Häse, and R.A.Finkelstein (1993).
Bacterial extracellular zinc-containing metalloproteases.
  Microbiol Rev, 57, 823-837.  
8229092 G.Vriend, and V.Eijsink (1993).
Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases.
  J Comput Aided Mol Des, 7, 367-396.  
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.