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PDBsum entry 1gbt
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Hydrolase(serine proteinase) PDB id
1gbt

 

 

 

 

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Contents
Protein chain
223 a.a. *
Ligands
SO4 ×2
GBS
Metals
_CA
Waters ×117
* Residue conservation analysis
PDB id:
1gbt
Name: Hydrolase(serine proteinase)
Title: Structure of an acyl-enzyme intermediate during catalysis: (guanidinobenzoyl) trypsin
Structure: Beta-trypsin. Chain: a. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913
Resolution:
2.00Å     R-factor:   0.162    
Authors: P.T.Singer,R.M.Sweet
Key ref:
W.F.Mangel et al. (1990). Structure of an acyl-enzyme intermediate during catalysis: (guanidinobenzoyl)trypsin. Biochemistry, 29, 8351-8357. PubMed id: 2252895 DOI: 10.1021/bi00488a022
Date:
17-Sep-91     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P00760  (TRY1_BOVIN) -  Serine protease 1 from Bos taurus
Seq:
Struc: 		246 a.a.
223 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.4  - trypsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

 

 
DOI no: 10.1021/bi00488a022 Biochemistry 29:8351-8357 (1990)
PubMed id: 2252895  
 
 
Structure of an acyl-enzyme intermediate during catalysis: (guanidinobenzoyl)trypsin.
W.F.Mangel, P.T.Singer, D.M.Cyr, T.C.Umland, D.L.Toledo, R.M.Stroud, J.W.Pflugrath, R.M.Sweet.
 
  ABSTRACT  
 
The crystal and molecular structure of trypsin at a transiently stable intermediate step during catalysis has been determined by X-ray diffraction methods. Bovine trypsin cleaved the substrate p-nitrophenyl p-guanidinobenzoate during crystallization under conditions in which the acyl-enzyme intermediate, (guanidinobenzoyl)trypsin, was stable. Orthorhombic crystals formed in space group P2(1)2(1)2(1), with a = 63.74, b = 63.54, and c = 68.93 A. This is a crystal form of bovine trypsin for which a molecular structure has not been reported. Diffraction data were measured with a FAST (Enraf Nonius) diffractometer. The structure was refined to a crystallographic residual of R = 0.16 for data in the resolution range 7.0-2.0 A. The refined model of (guanidinobenzoyl)trypsin provides insight into the structural basis for its slow rate of deacylation, which in solution at 25 degrees C and pH 7.4 exhibits a t1/2 of 12 h. In addition to the rotation of the Ser-195 hydroxyl away from His-157, C beta of Ser-195 moves 0.7 A toward Asp-189 at the bottom of the active site, with respect to the native structure. This allows formation of energetically favorable H bonds and an ion pair between the carboxylate of Asp-189 and the guanidino group of the substrate. This movement is dictated by the rigidity of the aromatic ring in guanidinobenzoate--model-building indicates that this should not occur when arginine, with its more flexible aliphatic backbone, forms the ester bond with Ser-195. As a consequence, highly ordered water molecules in the active site are no longer close enough to the scissile ester bond to serve as potential nucleophiles for hydrolysis.(ABSTRACT TRUNCATED AT 250 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
16492676 J.Tóth, L.Gombos, Z.Simon, P.Medveczky, L.Szilágyi, L.Gráf, and A.Málnási-Csizmadia (2006).
Thermodynamic analysis reveals structural rearrangement during the acylation step in human trypsin 4 on 4-methylumbelliferyl 4-guanidinobenzoate substrate analogue.
  J Biol Chem, 281, 12596-12602.  
15068800 K.Ponnuraj, Y.Xu, K.Macon, D.Moore, J.E.Volanakis, and S.V.Narayana (2004).
Structural analysis of engineered Bb fragment of complement factor B: insights into the activation mechanism of the alternative pathway C3-convertase.
  Mol Cell, 14, 17-28.
PDB codes: 1rrk 1rs0 1rtk
12808236 E.Toyota, H.Sekizaki, K.Itoh, and K.Tanizawa (2003).
Synthesis and evaluation of guanidine-containing Schiff base copper(II), zinc(II), and iron(III) chelates as trypsin inhibitors.
  Chem Pharm Bull (Tokyo), 51, 625-629.  
11731301 B.A.Katz, P.A.Sprengeler, C.Luong, E.Verner, K.Elrod, M.Kirtley, J.Janc, J.R.Spencer, J.G.Breitenbucher, H.Hui, D.McGee, D.Allen, A.Martelli, and R.L.Mackman (2001).
Engineering inhibitors highly selective for the S1 sites of Ser190 trypsin-like serine protease drug targets.
  Chem Biol, 8, 1107-1121.
PDB codes: 1gj4 1gj5 1gj6 1gj7 1gj8 1gj9 1gja 1gjb 1gjc 1gjd
9195866 J.A.Gerlt, M.M.Kreevoy, W.Cleland, and P.A.Frey (1997).
Understanding enzymic catalysis: the importance of short, strong hydrogen bonds.
  Chem Biol, 4, 259-267.  
8530349 M.Wilczynska, M.Fa, P.I.Ohlsson, and T.Ny (1995).
The inhibition mechanism of serpins. Evidence that the mobile reactive center loop is cleaved in the native protease-inhibitor complex.
  J Biol Chem, 270, 29652-29655.  
8595135 R.A.Engh, R.Huber, W.Bode, and A.J.Schulze (1995).
Divining the serpin inhibition mechanism: a suicide substrate 'springe'?
  Trends Biotechnol, 13, 503-510.  
15335767 D.Blow (1993).
Enzyme catalysis: now you see it, now you don't.
  Curr Biol, 3, 204-207.  
  1303743 L.N.Johnson (1992).
Time-resolved protein crystallography.
  Protein Sci, 1, 1237-1243.  
1729682 S.P.Bajaj, A.K.Sabharwal, J.Gorka, and J.J.Birktoft (1992).
Antibody-probed conformational transitions in the protease domain of human factor IX upon calcium binding and zymogen activation: putative high-affinity Ca(2+)-binding site in the protease domain.
  Proc Natl Acad Sci U S A, 89, 152-156.  
1881877 T.Earnest, E.Fauman, C.S.Craik, and R.Stroud (1991).
1.59 A structure of trypsin at 120 K: comparison of low temperature and room temperature structures.
  Proteins, 10, 171-187.
PDB code: 1dpo
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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