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PDBsum entry 1tm3
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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1tm3

 

 

 

 

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Contents
Protein chains
281 a.a. *
64 a.a. *
Ligands
CIT ×2
1PE ×3
Metals
_CA
_NA
Waters ×447
* Residue conservation analysis
PDB id:
1tm3
Name: Hydrolase
Title: Crystal structure of the complex of subtilisin bpn' with chymotrypsin inhibitor 2 m59k mutant
Structure: Subtilisin bpn' precursor. Chain: e. Synonym: subtilisin novo, alkaline protease. Engineered: yes. Mutation: yes. Chymotrypsin inhibitor 2. Chain: i. Engineered: yes. Mutation: yes
Source: Bacillus amyloliquefaciens. Organism_taxid: 1390. Gene: apr. Expressed in: bacillus subtilis. Expression_system_taxid: 1423. Hordeum vulgare subsp. Vulgare. Domesticated barley. Organism_taxid: 112509. Strain: subsp. Vulgare.
Biol. unit: Dimer (from PQS)
Resolution:
1.57Å     R-factor:   0.167     R-free:   0.184
Authors: E.S.Radisky,G.Kwan,C.J.Karen Lu,D.E.Koshland Jr.
Key ref:
E.S.Radisky et al. (2004). Binding, proteolytic, and crystallographic analyses of mutations at the protease-inhibitor interface of the subtilisin BPN'/chymotrypsin inhibitor 2 complex. Biochemistry, 43, 13648-13656. PubMed id: 15504027 DOI: 10.1021/bi048797k
Date:
10-Jun-04     Release date:   09-Nov-04    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00782  (SUBT_BACAM) -  Subtilisin BPN' from Bacillus amyloliquefaciens
Seq:
Struc: 		382 a.a.
281 a.a.
Protein chain
Pfam   ArchSchema ?
Q40059  (Q40059_HORVU) -  Chymotrypsin inhibitor 2 from Hordeum vulgare
Seq:
Struc: 		84 a.a.
64 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chain E: E.C.3.4.21.62  - subtilisin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1. Hydrolyzes peptide amides.

 

 
DOI no: 10.1021/bi048797k Biochemistry 43:13648-13656 (2004)
PubMed id: 15504027  
 
 
Binding, proteolytic, and crystallographic analyses of mutations at the protease-inhibitor interface of the subtilisin BPN'/chymotrypsin inhibitor 2 complex.
E.S.Radisky, G.Kwan, C.J.Karen Lu, D.E.Koshland.
 
  ABSTRACT  
 
A series of mutants of chymotrypsin inhibitor 2 (CI2), at residues that interact with the inhibited enzyme subtilisin BPN', were studied to determine the relative importance of intermolecular contacts on either side of the scissile bond. Mutants were tested for inhibition of subtilisin, rates of hydrolysis by subtilisin, and ability to acylate subtilisin. Additionally, crystal structures of the mutant CI2 complexes with subtilisin were obtained. Ordered water molecules were found to play an important role in inhibitor recognition, and features of the crystal structures, in combination with biochemical data, support a transition-state stabilization role for the P(1) residue in subtilisin catalysis. Consistent with the proposed mechanism of inhibition, in which rapid acylation is followed by religation, leaving-group contacts with the enzyme were found to be more critical determinants of inhibition than acylating-group contacts in the mutants studied here.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21287622 M.J.Whitley, and A.L.Lee (2011).
Exploring the role of structure and dynamics in the function of chymotrypsin inhibitor 2.
  Proteins, 79, 916-924.  
20541512 J.Vévodová, M.Gamble, G.Künze, A.Ariza, E.Dodson, D.D.Jones, and K.S.Wilson (2010).
Crystal structure of an intracellular subtilisin reveals novel structural features unique to this subtilisin family.
  Structure, 18, 744-755.
PDB codes: 2wv7 2wwt 2x8j
20231898 R.Bourgeas, M.J.Basse, X.Morelli, and P.Roche (2010).
Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database.
  PLoS One, 5, e9598.  
  20073082 S.Khamrui, S.Majumder, J.Dasgupta, J.K.Dattagupta, and U.Sen (2010).
Identification of a novel set of scaffolding residues that are instrumental for the inhibitory property of Kunitz (STI) inhibitors.
  Protein Sci, 19, 593-602.
PDB codes: 3i2a 3i2x
19761257 T.Gallagher, B.Ruan, M.London, M.A.Bryan, and P.N.Bryan (2009).
Structure of a switchable subtilisin complexed with a substrate and with the activator azide.
  Biochemistry, 48, 10389-10394.
PDB codes: 3bgo 3co0
18077447 M.A.Salameh, A.S.Soares, A.Hockla, and E.S.Radisky (2008).
Structural basis for accelerated cleavage of bovine pancreatic trypsin inhibitor (BPTI) by human mesotrypsin.
  J Biol Chem, 283, 4115-4123.
PDB codes: 2r9p 2ra3
17157870 W.M.Hanson, G.J.Domek, M.P.Horvath, and D.P.Goldenberg (2007).
Rigidification of a flexible protease inhibitor variant upon binding to trypsin.
  J Mol Biol, 366, 230-243.
PDB codes: 2ftl 2ftm
16636277 E.S.Radisky, J.M.Lee, C.J.Lu, and D.E.Koshland (2006).
Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates.
  Proc Natl Acad Sci U S A, 103, 6835-6840.
PDB codes: 2age 2agg 2agi 2ah4
16367748 R.Helland, A.N.Larsen, A.O.Smalås, and N.P.Willassen (2006).
The 1.8 A crystal structure of a proteinase K-like enzyme from a psychrotroph Serratia species.
  FEBS J, 273, 61-71.
PDB code: 2b6n
15987886 M.Jäger, X.Michalet, and S.Weiss (2005).
Protein-protein interactions as a tool for site-specific labeling of proteins.
  Protein Sci, 14, 2059-2068.  
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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