spacer
spacer

PDBsum entry 1gmc
Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1gmc

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
11 a.a.
131 a.a. *
95 a.a. *
Ligands
PRO-GLY-ALA-TYR
Waters ×97
* Residue conservation analysis
PDB id:
1gmc
Name: Hydrolase
Title: The x-ray crystal structure of the tetrahedral intermediate of gamma- chymotrypsin in hexane
Structure: Gamma-chymotrypsin a. Chain: e. Gamma-chymotrypsin a. Chain: f. Gamma-chymotrypsin a. Chain: g. Pro gly ala tyr peptide. Chain: b
Source: Bos taurus. Cattle. Organism_taxid: 9913.
Biol. unit: Octamer (from PQS)
Resolution:
2.20Å     R-factor:   0.176    
Authors: N.H.Yennawar,H.P.Yennawar,S.Banerjee,G.K.Farber
Key ref:
N.H.Yennawar et al. (1994). X-ray crystal structure of gamma-chymotrypsin in hexane. Biochemistry, 33, 7326-7336. PubMed id: 8003497 DOI: 10.1021/bi00189a038
Date:
20-Aug-93     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Enzyme reactions 
   Enzyme class: Chains E, F, G: E.C.3.4.21.1  - chymotrypsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Tyr-|-Xaa, Trp-|-Xaa, Phe-|-Xaa, Leu-|-Xaa.

 

 
DOI no: 10.1021/bi00189a038 Biochemistry 33:7326-7336 (1994)
PubMed id: 8003497  
 
 
X-ray crystal structure of gamma-chymotrypsin in hexane.
N.H.Yennawar, H.P.Yennawar, G.K.Farber.
 
  ABSTRACT  
 
Crystals of gamma-chymotrypsin grown in aqueous solution were soaked in n-hexane, and the structures of both the soaked and the native crystals were determined to 2.2-A resolution. Seven hexane molecules and 130 water molecules were found in the hexane-soaked crystals. Two of the seven hexane molecules are found near the active site, and the rest are close to hydrophobic regions on or near the surface of the enzyme. In the hexane structure, water molecules that were not observed in the native structure form a clathrate around one of the hexane molecules. Only 97 water molecules were found in the native structure. The temperature factors for atoms in the hexane environment are lower than those in the aqueous environment. There are significant changes between the two structures in the side chains of both polar and neutral residues, particularly in the vicinity of the hexane molecules. These changes have perturbed the hydrogen-bonding patterns. The electron density for the peptide bound in the active site has been dramatically altered in hexane and appears to be tetrahedral at the carbon that is covalently bound to Ser 195. The crystalline enzyme retains its active conformation in the nonpolar medium and can catalyze both hydrolysis and synthesis reactions in hexane.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19066990 J.J.Stewart (2009).
Application of the PM6 method to modeling proteins.
  J Mol Model, 15, 765-805.  
18254946 P.Trodler, and J.Pleiss (2008).
Modeling structure and flexibility of Candida antarctica lipase B in organic solvents.
  BMC Struct Biol, 8, 9.  
17372355 M.Sherawat, P.Kaur, M.Perbandt, C.Betzel, W.A.Slusarchyk, G.S.Bisacchi, C.Chang, B.L.Jacobson, H.M.Einspahr, and T.P.Singh (2007).
Structure of the complex of trypsin with a highly potent synthetic inhibitor at 0.97 A resolution.
  Acta Crystallogr D Biol Crystallogr, 63, 500-507.
PDB code: 2ayw
17419728 N.M.Micaêlo, and C.M.Soares (2007).
Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents.
  FEBS J, 274, 2424-2436.  
17187678 B.Castillo, V.Bansal, A.Ganesan, P.Halling, F.Secundo, A.Ferrer, K.Griebenow, and G.Barletta (2006).
On the activity loss of hydrolases in organic solvents: II. a mechanistic study of subtilisin Carlsberg.
  BMC Biotechnol, 6, 51.  
16754679 B.Liu, C.J.Schofield, and R.C.Wilmouth (2006).
Structural analyses on intermediates in serine protease catalysis.
  J Biol Chem, 281, 24024-24035.
PDB codes: 2bb4 2bd2 2bd3 2bd4 2bd5 2bd7 2bd8 2bd9 2bda 2bdb 2bdc 2h1u
16641296 C.E.Zeitler, M.K.Estes, and B.V.Venkataram Prasad (2006).
X-ray crystallographic structure of the Norwalk virus protease at 1.5-A resolution.
  J Virol, 80, 5050-5058.
PDB codes: 2fyq 2fyr
15654893 N.Singh, T.Jabeen, S.Sharma, I.Roy, M.N.Gupta, S.Bilgrami, R.K.Somvanshi, S.Dey, M.Perbandt, C.Betzel, A.Srinivasan, and T.P.Singh (2005).
Detection of native peptides as potent inhibitors of enzymes. Crystal structure of the complex formed between treated bovine alpha-chymotrypsin and an autocatalytically produced fragment, IIe-Val-Asn-Gly-Glu-Glu-Ala-Val-Pro-Gly-Ser-Trp-Pro-Trp, at 2.2 angstroms resolution.
  FEBS J, 272, 562-572.
PDB code: 1oxg
15690493 Y.P.Pang (2004).
Three-dimensional model of a substrate-bound SARS chymotrypsin-like cysteine proteinase predicted by multiple molecular dynamics simulations: catalytic efficiency regulated by substrate binding.
  Proteins, 57, 747-757.
PDB codes: 1p76 2aj5
12609866 C.M.Soares, V.H.Teixeira, and A.M.Baptista (2003).
Protein structure and dynamics in nonaqueous solvents: insights from molecular dynamics simulation studies.
  Biophys J, 84, 1628-1641.  
12962630 J.R.Somoza, J.D.Ho, C.Luong, M.Ghate, P.A.Sprengeler, K.Mortara, W.D.Shrader, D.Sperandio, H.Chan, M.E.McGrath, and B.A.Katz (2003).
The structure of the extracellular region of human hepsin reveals a serine protease domain and a novel scavenger receptor cysteine-rich (SRCR) domain.
  Structure, 11, 1123-1131.
PDB code: 1p57
11257512 G.Zhu, Q.Huang, Y.Zhu, Y.Li, C.Chi, and Y.Tang (2001).
X-Ray study on an artificial mung bean inhibitor complex with bovine beta-trypsin in neat cyclohexane.
  Biochim Biophys Acta, 1546, 98.
PDB code: 1g9i
11514565 N.C.Rockwell, and R.S.Fuller (2001).
Differential utilization of enzyme-substrate interactions for acylation but not deacylation during the catalytic cycle of Kex2 protease.
  J Biol Chem, 276, 38394-38399.  
11342057 V.V.Gorbatchuk, M.A.Ziganshin, N.A.Mironov, and B.N.Solomonov (2001).
Homotropic cooperative binding of organic solvent vapors by solid trypsin.
  Biochim Biophys Acta, 1545, 326-338.  
11134922 W.R.Rypniewski, P.R.Ostergaard, M.Nørregaard-Madsen, M.Dauter, and K.S.Wilson (2001).
Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding.
  Acta Crystallogr D Biol Crystallogr, 57, 8.
PDB codes: 1fn8 1fy4 1fy5 1gdn 1gdq 1gdu
10992230 G.A.Hutcheon, M.C.Parker, and B.D.Moore (2000).
Measuring enzyme motility in organic media using novel H-D exchange methodology.
  Biotechnol Bioeng, 70, 262-269.  
10679381 G.A.Petsko, and D.Ringe (2000).
Observation of unstable species in enzyme-catalyzed transformations using protein crystallography.
  Curr Opin Chem Biol, 4, 89-94.  
10651278 A.C.English, S.H.Done, L.S.Caves, C.R.Groom, and R.E.Hubbard (1999).
Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol.
  Proteins, 37, 628-640.
PDB codes: 1tli 1tlx 2tli 2tlx 3tli 4tli 5tli 6tli 7tli 8tli
10665832 G.K.Farber (1999).
New approaches to rational drug design.
  Pharmacol Ther, 84, 327-332.  
10099631 P.Pepin, and R.Lortie (1999).
Influence of water activity on the enantioselective esterification of (R,S)-ibuprofen by Candida antarctica lipase B in solventless media.
  Biotechnol Bioeng, 63, 502-505.  
10468562 X.G.Gao, E.Maldonado, R.Pérez-Montfort, G.Garza-Ramos, M.T.de Gómez-Puyou, A.Gómez-Puyou, and A.Rodríguez-Romero (1999).
Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane.
  Proc Natl Acad Sci U S A, 96, 10062-10067.
PDB code: 1ci1
10380349 Y.Shimohigashi, T.Nose, Y.Yamauchi, and I.Maeda (1999).
Design of serine protease inhibitors with conformation restricted by amino acid side-chain-side-chain CH/pie interaction.
  Biopolymers, 51, 9.  
9818266 B.L.Stoddard (1998).
New results using Laue diffraction and time-resolved crystallography.
  Curr Opin Struct Biol, 8, 612-618.  
9789015 J.L.Schmitke, L.J.Stern, and A.M.Klibanov (1998).
Comparison of x-ray crystal structures of an acyl-enzyme intermediate of subtilisin Carlsberg formed in anhydrous acetonitrile and in water.
  Proc Natl Acad Sci U S A, 95, 12918-12923.
PDB codes: 1be6 1be8
9649306 Y.A.Puius, M.Zou, N.T.Ho, C.Ho, and S.C.Almo (1998).
Novel water-mediated hydrogen bonds as the structural basis for the low oxygen affinity of the blood substitute candidate rHb(alpha 96Val-->Trp).
  Biochemistry, 37, 9258-9265.
PDB codes: 1rvw 1vwt
9080715 A.M.Klibanov (1997).
Why are enzymes less active in organic solvents than in water?
  Trends Biotechnol, 15, 97.  
9109667 C.S.Cassidy, J.Lin, and P.A.Frey (1997).
A new concept for the mechanism of action of chymotrypsin: the role of the low-barrier hydrogen bond.
  Biochemistry, 36, 4576-4584.  
  9260285 J.Dunbar, H.P.Yennawar, S.Banerjee, J.Luo, and G.K.Farber (1997).
The effect of denaturants on protein structure.
  Protein Sci, 6, 1727-1733.
PDB codes: 1ddr 1dds 1rbw 1rbx
9253408 J.E.Murphy, B.Stec, L.Ma, and E.R.Kantrowitz (1997).
Trapping and visualization of a covalent enzyme-phosphate intermediate.
  Nat Struct Biol, 4, 618-622.
PDB code: 1hjk
9113975 J.L.Schmitke, L.J.Stern, and A.M.Klibanov (1997).
The crystal structure of subtilisin Carlsberg in anhydrous dioxane and its comparison with those in water and acetonitrile.
  Proc Natl Acad Sci U S A, 94, 4250-4255.
PDB code: 1af4
18634023 K.Griebenow, and A.M.Klibanov (1997).
Can conformational changes be responsible for solvent and excipient effects on the catalytic behavior of subtilisin Carlsberg in organic solvents?
  Biotechnol Bioeng, 53, 351-362.  
8673602 B.L.Stoddard, A.Dean, and P.A.Bash (1996).
Combining Laue diffraction and molecular dynamics to study enzyme intermediates.
  Nat Struct Biol, 3, 590-595.  
8888067 B.L.Stoddard (1996).
Intermediate trapping and laue X-ray diffraction: potential for enzyme mechanism, dynamics, and inhibitor screening.
  Pharmacol Ther, 70, 215-256.  
21121013 Y.J.Zheng, and R.L.Ornstein (1996).
Molecular dynamics of subtilisin Carlsberg in aqueous and nonaqueous solutions.
  Biopolymers, 38, 791-799.  
8590009 B.L.Stoddard, and G.K.Farber (1995).
Direct measurement of reactivity in the protein crystal by steady-state kinetic studies.
  Structure, 3, 991-996.  
8548273 G.K.Farber (1995).
Laue crystallography. It's show time.
  Curr Biol, 5, 1088-1090.  
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.

 

spacer
spacer