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Hydrolase (serine proteinase) PDB id
1gbe
Jmol
Contents
Protein chain
198 a.a. *
Ligands
SO4 ×2
Waters ×173
* Residue conservation analysis
PDB id:
1gbe
Name: Hydrolase (serine proteinase)
Title: Alpha-lytic protease with met 190 replaced by ala and gly 216 replaced by leu
Structure: Alpha-lytic protease. Chain: a. Engineered: yes. Mutation: yes
Source: Lysobacter enzymogenes. Organism_taxid: 69. Strain: 495. Atcc: 29487. Gene: alpha-lytic protease preproenz. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.30Å     R-factor:   0.141    
Authors: J.E.Mace,D.A.Agard
Key ref:
J.E.Mace and D.A.Agard (1995). Kinetic and structural characterization of mutations of glycine 216 in alpha-lytic protease: a new target for engineering substrate specificity. J Mol Biol, 254, 720-736. PubMed id: 7500345 DOI: 10.1006/jmbi.1995.0650
Date:
06-Sep-95     Release date:   29-Jan-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00778  (PRLA_LYSEN) -  Alpha-lytic protease
Seq:
Struc: 		397 a.a.
198 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.12  - Alpha-lytic endopeptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of proteins, especially bonds adjacents to L-alanine and L-valine residues in bacterial cell walls, elastin and other proteins.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
DOI no: 10.1006/jmbi.1995.0650 J Mol Biol 254:720-736 (1995)
PubMed id: 7500345  
 
 
Kinetic and structural characterization of mutations of glycine 216 in alpha-lytic protease: a new target for engineering substrate specificity.
J.E.Mace, D.A.Agard.
 
  ABSTRACT  
 
Gly216 in the active site of the broadly specific MA190 mutant of alpha-lytic protease has been found to be remarkably tolerant of amino acid substitutions. Side-chains as large as Trp can be accommodated within the substrate-binding pocket without abolishing catalysis, and have major effects upon the substrate specificity of the enzyme. Kinetic characterization of eleven enzymatically active mutants against a panel of eight substrates clearly revealed the functional consequences of the substitutions at position 216. To understand better the structural basis for their altered specificity, the GA216 + MA190 and GL216 + MA190 mutants have been crystallized both with and without a representative series of peptide boronic acid transition-state analog inhibitors. An empirical description and non-parametric statistical analysis of structural variation among these enzyme: inhibitor complexes is presented. The roles of active site plasticity and dynamics in alpha-lytic protease function and substrate preference are also addressed. The results strongly suggest that substrate specificity determination in alpha-lytic protease is a distributed property of the active site and substrate molecule.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Superimposed structures of the a-lytic protease active site in the absence of inhibitor, showing the localized structural perturbations due to mutation of Gly216. Red, MA190; blue, GA216 + MA190; yellow, GL216 + MA190. This image (as well as those in Figures 5 and 6) was prepared with Raster3D (Merritt & Murphy, 1994).
 
  The above figure is reprinted by permission from Elsevier: J Mol Biol (1995, 254, 720-736) copyright 1995.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20179339 T.C.Terwilliger (2010).
Rapid model building of beta-sheets in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 276-284.  
19562127 N.J.Deng, and P.Cieplak (2009).
Insights into affinity and specificity in the complexes of alpha-lytic protease and its inhibitor proteins: binding free energy from molecular dynamics simulation.
  Phys Chem Chem Phys, 11, 4968-4981.  
16044461 S.M.Truhlar, and D.A.Agard (2005).
The folding landscape of an alpha-lytic protease variant reveals the role of a conserved beta-hairpin in the development of kinetic stability.
  Proteins, 61, 105-114.  
14739318 E.L.Cunningham, and D.A.Agard (2004).
Disabling the folding catalyst is the last critical step in alpha-lytic protease folding.
  Protein Sci, 13, 325-331.  
12483203 G.M.Süel, S.W.Lockless, M.A.Wall, and R.Ranganathan (2003).
Evolutionarily conserved networks of residues mediate allosteric communication in proteins.
  Nat Struct Biol, 10, 59-69.  
11420442 N.Ota, and D.A.Agard (2001).
Enzyme specificity under dynamic control II: Principal component analysis of alpha-lytic protease using global and local solvent boundary conditions.
  Protein Sci, 10, 1403-1414.  
9601029 J.H.Davis, and D.A.Agard (1998).
Relationship between enzyme specificity and the backbone dynamics of free and inhibited alpha-lytic protease.
  Biochemistry, 37, 7696-7707.  
9724517 R.J.Peters, A.K.Shiau, J.L.Sohl, D.E.Anderson, G.Tang, J.L.Silen, and D.A.Agard (1998).
Pro region C-terminus:protease active site interactions are critical in catalyzing the folding of alpha-lytic protease.
  Biochemistry, 37, 12058-12067.
PDB code: 1boq
9660802 S.Kawaguchi, and S.Kuramitsu (1998).
Thermodynamics and molecular simulation analysis of hydrophobic substrate recognition by aminotransferases.
  J Biol Chem, 273, 18353-18364.  
9836602 S.R.Presnell, G.S.Patil, C.Mura, K.M.Jude, J.M.Conley, J.A.Bertrand, C.M.Kam, J.C.Powers, and L.D.Williams (1998).
Oxyanion-mediated inhibition of serine proteases.
  Biochemistry, 37, 17068-17081.
PDB codes: 1bju 1bjv
9374470 J.J.Perona, and C.S.Craik (1997).
Evolutionary divergence of substrate specificity within the chymotrypsin-like serine protease fold.
  J Biol Chem, 272, 29987-29990.  
9092819 J.L.Sohl, A.K.Shiau, S.D.Rader, B.J.Wilk, and D.A.Agard (1997).
Inhibition of alpha-lytic protease by pro region C-terminal steric occlusion of the active site.
  Biochemistry, 36, 3894-3902.  
  9232638 S.D.Rader, and D.A.Agard (1997).
Conformational substates in enzyme mechanism: the 120 K structure of alpha-lytic protease at 1.5 A resolution.
  Protein Sci, 6, 1375-1386.
PDB codes: 1tal 2ull
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.