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Hydrolase/hydrolase inhibitor PDB id
1p10
Jmol
Contents
Protein chain
198 a.a. *
Ligands
ALA-ALA-PRO-B2V
SO4
Waters ×148
* Residue conservation analysis
PDB id:
1p10
Name: Hydrolase/hydrolase inhibitor
Title: Structural plasticity as a determinant of enzyme specificity broadly specific proteases
Structure: Alpha-lytic protease. Chain: a. Engineered: yes. Methoxysuccinyl-ala-ala-pro-valine boronic acid i chain: p. Engineered: yes
Source: Lysobacter enzymogenes. Organism_taxid: 69. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes
Resolution:
2.25Å     R-factor:   0.144    
Authors: R.Bone,D.A.Agard
Key ref: R.Bone et al. (1989). Structural plasticity broadens the specificity of an engineered protease. Nature, 339, 191-195. PubMed id: 2716847 DOI: 10.1038/339191a0
Date:
24-Apr-89     Release date:   15-Apr-90    
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 1 residue position (black cross)

 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: 10.1038/339191a0 Nature 339:191-195 (1989)
PubMed id: 2716847  
 
 
Structural plasticity broadens the specificity of an engineered protease.
R.Bone, J.L.Silen, D.A.Agard.
 
  ABSTRACT  
 
The substrate specificity of alpha-lytic protease has been changed dramatically, with a concomitant increase in activity, by replacing an active-site Met with Ala. The substrate specificity of both this mutant and another similar mutant are extraordinarily broad. X-ray crystallographic analysis shows that structural plasticity, a combination of alternate side-chain conformations and binding-site flexibility, allows both large and small substrates to be well accommodated.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors.
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PDB codes: 1jui 1jyc
11320244 J.S.Marvin, and H.W.Hellinga (2001).
Conversion of a maltose receptor into a zinc biosensor by computational design.
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11410858 S.Lien, S.J.Milner, L.D.Graham, J.C.Wallace, and G.L.Francis (2001).
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10500147 H.Ma, and T.M.Penning (1999).
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Redesigning the substrate specificity of an enzyme by cumulative effects of the mutations of non-active site residues.
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PDB code: 1yoo
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9808037 N.K.Sauter, T.Mau, S.D.Rader, and D.A.Agard (1998).
Structure of alpha-lytic protease complexed with its pro region.
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PDB codes: 2pro 3pro 4pro
9548762 O.R.Veltman, V.G.Eijsink, G.Vriend, A.de Kreij, G.Venema, and B.Van den Burg (1998).
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9013553 B.X.Yan, and Y.Q.Sun (1997).
Glycine residues provide flexibility for enzyme active sites.
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9154921 C.A.Tsu, J.J.Perona, R.J.Fletterick, and C.S.Craik (1997).
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9374470 J.J.Perona, and C.S.Craik (1997).
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PDB codes: 1tal 2ull
8756473 A.R.Welch, C.M.Holman, M.Huber, M.C.Brenner, M.F.Browner, and H.E.Van Wart (1996).
Understanding the P1' specificity of the matrix metalloproteinases: effect of S1' pocket mutations in matrilysin and stromelysin-1.
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Structural basis of substrate specificity in the serine proteases.
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PDB code: 1amh
7785837 L.D.Graham, K.D.Haggett, P.J.Hayes, P.A.Schober, P.A.Jennings, and R.G.Whittaker (1995).
Random mutagenesis of the substrate-binding site of a serine protease. A new library of alpha-lytic protease S1 mutants.
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Replacements in a conserved leucine cluster in the hydrophobic heme pocket of cytochrome c.
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PDB codes: 1csu 1csv 1csw 1csx
7989570 E.L.Madison (1994).
Studies of serpins unfold at a feverish pace.
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8183880 J.A.Wells, W.J.Fairbrother, J.Otlewski, M.Laskowski, and J.Burnier (1994).
A reinvestigation of a synthetic peptide (TrPepz) designed to mimic trypsin.
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Structure and selectivity of a monovalent cation binding site in cubic insulin crystals.
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Molecular recognition analyzed by docking simulations: the aspartate receptor and isocitrate dehydrogenase from Escherichia coli.
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7680808 B.Tidor, and M.Karplus (1993).
The contribution of cross-links to protein stability: a normal mode analysis of the configurational entropy of the native state.
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Expression of virus-encoded proteinases: functional and structural similarities with cellular enzymes.
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1618906 A.Fujishige, K.R.Smith, J.L.Silen, and D.A.Agard (1992).
Correct folding of alpha-lytic protease is required for its extracellular secretion from Escherichia coli.
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1409689 L.W.Hardy, and E.Nalivaika (1992).
Asn177 in Escherichia coli thymidylate synthase is a major determinant of pyrimidine specificity.
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  1367680 A.Pastore, and A.M.Lesk (1991).
Brave new proteins: what evolution reveals about protein structure.
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1924337 G.B.Henderson, N.J.Murgolo, J.Kuriyan, K.Osapay, D.Kominos, A.Berry, N.S.Scrutton, N.W.Hinchliffe, R.N.Perham, and A.Cerami (1991).
Engineering the substrate specificity of glutathione reductase toward that of trypanothione reduction.
  Proc Natl Acad Sci U S A, 88, 8769-8773.  
2023950 M.Meng, C.Lee, M.Bagdasarian, and J.G.Zeikus (1991).
Switching substrate preference of thermophilic xylose isomerase from D-xylose to D-glucose by redesigning the substrate binding pocket.
  Proc Natl Acad Sci U S A, 88, 4015-4019.  
1755827 R.N.Perham, N.S.Scrutton, and A.Berry (1991).
New enzymes for old: redesigning the coenzyme and substrate specificities of glutathione reductase.
  Bioessays, 13, 515-525.  
1651245 T.Tron, M.Crimi, A.M.Colson, and M.Degli Esposti (1991).
Structure/function relationships in mitochondrial cytochrome b revealed by the kinetic and circular dichroic properties of two yeast inhibitor-resistant mutants.
  Eur J Biochem, 199, 753-760.  
  1366953 W.S.Sandberg, and T.C.Terwilliger (1991).
Repacking protein interiors.
  Trends Biotechnol, 9, 59-63.  
2183216 J.J.Burbaum, R.M.Starzyk, and P.Schimmel (1990).
Understanding structural relationships in proteins of unsolved three-dimensional structure.
  Proteins, 7, 99.  
2204062 L.B.Evnin, J.R.Vásquez, and C.S.Craik (1990).
Substrate specificity of trypsin investigated by using a genetic selection.
  Proc Natl Acad Sci U S A, 87, 6659-6663.  
1692343 R.S.Eisenberg (1990).
Channels as enzymes.
  J Membr Biol, 115, 1.  
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.