PDBsum entry 2gmt

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase(serine proteinase) PDB id
Protein chains
131 a.a.
95 a.a.
Waters ×238
PDB id:
Name: Hydrolase(serine proteinase)
Title: Three-dimensional structure of chymotrypsin inactivated with acetyl-l-alanyl-l-phenylalanyl-chloroethyl ketone: implicat the mechanism of inactivation of serine proteases by chloro
Structure: Gamma-chymotrypsin. Chain: a. Engineered: yes. Gamma-chymotrypsin. Chain: b. Gamma-chymotrypsin. Chain: c. Ec:
Source: Bos taurus. Cattle. Organism_taxid: 9913.
Biol. unit: Dimer (from PQS)
1.80Å     R-factor:   0.188    
Authors: K.Kreutter,A.C.U.Steinmetz,T.-C.Liang,M.Prorok,R.Abeles,D.Ri
Key ref:
K.Kreutter et al. (1994). Three-dimensional structure of chymotrypsin inactivated with (2S)-N-acetyl-L-alanyl-L-phenylalanyl alpha-chloroethane: implications for the mechanism of inactivation of serine proteases by chloroketones. Biochemistry, 33, 13792-13800. PubMed id: 7947790 DOI: 10.1021/bi00250a033
07-Sep-94     Release date:   01-Nov-94    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00766  (CTRA_BOVIN) -  Chymotrypsinogen A
245 a.a.
131 a.a.
Protein chain
Pfam   ArchSchema ?
P00766  (CTRA_BOVIN) -  Chymotrypsinogen A
245 a.a.
95 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1021/bi00250a033 Biochemistry 33:13792-13800 (1994)
PubMed id: 7947790  
Three-dimensional structure of chymotrypsin inactivated with (2S)-N-acetyl-L-alanyl-L-phenylalanyl alpha-chloroethane: implications for the mechanism of inactivation of serine proteases by chloroketones.
K.Kreutter, A.C.Steinmetz, T.C.Liang, M.Prorok, R.H.Abeles, D.Ringe.
The reaction of enantiomerically pure (2S)-N-acetyl-L-alanyl-L-phenylalanyl alpha-chloroethane with gamma-chymotrypsin was studied as a probe of the mechanism of inactivation of serine proteases by peptidyl chloroalkanes. It was determined crystallographically that the peptidyl chloroethane alkylates His57 with retention of configuration at the chiral center, indicating a double displacement mechanism. We think it likely that a Ser195-epoxy ether adduct is an intermediate on the inactivation pathway, although other possibilities have not been disproven. Kinetic data reported by others [Angliker et al. (1988) Biochem. J. 256, 481-486] indicate that the epoxy ether intermediate is not an irreversibly inactivated form of enzyme [a conclusion confirmed experimentally (Prorok et al. (1994) Biochemistry 33, 9784-9790)] and that both ring closure of the tetrahedral intermediate to form the epoxy ether and ring opening by His57 partially limit the first-order rate constant for inactivation, ki. The peptidyl chloroethyl derivative adopts a very different active site conformation from that assumed by serine proteases inactivated by peptidyl chloromethanes. Positioning the chloroethyl derivative into the conformation adopted by chloromethyl derivatives would cause the extra methyl group to make a bad van der Waals contact with the inactivator P2 carbonyl carbon, thereby preventing the formation of the invariant hydrogen bond between the inactivator P1 amide nitrogen and the carbonyl group of Ser214. We conclude that the unusual conformation displayed by the chloroethyl derivative is caused by steric hindrance between the extra methyl group and the rest of the inactivator chain.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20014086 B.Knuckley, C.P.Causey, P.J.Pellechia, P.F.Cook, and P.R.Thompson (2010).
Haloacetamidine-based inactivators of protein arginine deiminase 4 (PAD4): evidence that general acid catalysis promotes efficient inactivation.
  Chembiochem, 11, 161-165.  
10611646 J.D.Tyndall, and D.P.Fairlie (1999).
Conformational homogeneity in molecular recognition by proteolytic enzymes.
  J Mol Recognit, 12, 363-370.  
9622503 K.D.Brady (1998).
Bimodal inhibition of caspase-1 by aryloxymethyl and acyloxymethyl ketones.
  Biochemistry, 37, 8508-8515.  
9208091 T.S.Morris, S.Frormann, S.Shechosky, C.Lowe, M.S.Lall, V.Gauss-Müller, R.H.Purcell, S.U.Emerson, J.C.Vederas, and B.A.Malcolm (1997).
In vitro and ex vivo inhibition of hepatitis A virus 3C proteinase by a peptidyl monofluoromethyl ketone.
  Bioorg Med Chem, 5, 797-807.  
8968955 N.Mukerjee, M.Dryjanski, W.Dai, J.A.Katzenellenbogen, and R.Pietruszko (1996).
Haloenol lactones as inactivators and substrates of aldehyde dehydrogenase.
  J Protein Chem, 15, 639-648.  
8894108 W.P.Taylor, Z.Y.Zhang, and T.S.Widlanski (1996).
Quiescent affinity inactivators of protein tyrosine phosphatases.
  Bioorg Med Chem, 4, 1515-1520.  
7642593 F.Jean, A.Boudreault, A.Basak, N.G.Seidah, and C.Lazure (1995).
Fluorescent peptidyl substrates as an aid in studying the substrate specificity of human prohormone convertase PC1 and human furin and designing a potent irreversible inhibitor.
  J Biol Chem, 270, 19225-19231.  
7797466 P.J.Lenting, H.ter Maat, P.P.Clijsters, M.J.Donath, J.A.van Mourik, and K.Mertens (1995).
Cleavage at arginine 145 in human blood coagulation factor IX converts the zymogen into a factor VIII binding enzyme.
  J Biol Chem, 270, 14884-14890.  
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.