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PDBsum entry 1esb
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Hydrolase PDB id
1esb

 

 

 

 

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Contents
Protein chain
240 a.a. *
Ligands
BBL
SO4
Metals
_CA
Waters ×126
* Residue conservation analysis
PDB id:
1esb
Name: Hydrolase
Title: Direct structure observation of an acyl-enzyme intermediate in the hydrolysis of an ester substrate by elastase
Structure: Porcine pancreatic elastase. Chain: a. Engineered: yes
Source: Sus scrofa. Pig. Organism_taxid: 9823
Resolution:
2.30Å     R-factor:   0.210    
Authors: X.Ding,B.Rasmussen,G.A.Petsko,D.Ringe
Key ref:
X.Ding et al. (1994). Direct structural observation of an acyl-enzyme intermediate in the hydrolysis of an ester substrate by elastase. Biochemistry, 33, 9285-9293. PubMed id: 8049229 DOI: 10.1021/bi00197a032
Date:
04-Feb-94     Release date:   30-Apr-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00772  (CELA1_PIG) -  Chymotrypsin-like elastase family member 1 from Sus scrofa
Seq:
Struc: 		266 a.a.
240 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.3.4.21.36  - pancreatic elastase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of proteins, including elastin. Preferential cleavage: Ala-|-Xaa.

 

 
DOI no: 10.1021/bi00197a032 Biochemistry 33:9285-9293 (1994)
PubMed id: 8049229  
 
 
Direct structural observation of an acyl-enzyme intermediate in the hydrolysis of an ester substrate by elastase.
X.Ding, B.F.Rasmussen, G.A.Petsko, D.Ringe.
 
  ABSTRACT  
 
The method of X-ray crystallographic cryoenzymology has been used to determine the crystal structure of a kinetically significant species on the reaction pathway of a crystalline enzyme. The structure of a specific acyl-enzyme intermediate in the elastase-catalyzed hydrolysis of the N-carbobenzoxy-L-alanine p-nitrophenyl ester has been determined and refined against X-ray diffraction data at 2.3-A resolution. The difference Fourier electron density map clearly shows electron density for the trapped acyl-enzyme. The acyl-enzyme was formed at -26 degrees C and was stabilized at -55 degrees C during data collection, taking advantage of the glass transition in protein dynamics that occurs at around -50 degrees C.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22785315 T.Nakamura, Y.Zhao, Y.Yamagata, Y.J.Hua, and W.Yang (2012).
Watching DNA polymerase η make a phosphodiester bond.
  Nature, 487, 196-201.
PDB codes: 4ecq 4ecr 4ecs 4ect 4ecu 4ecv 4ecw 4ecx 4ecy 4ecz 4ed0 4ed1 4ed2 4ed3 4ed6 4ed7 4ed8
19549826 E.Zakharova, M.P.Horvath, and D.P.Goldenberg (2009).
Structure of a serine protease poised to resynthesize a peptide bond.
  Proc Natl Acad Sci U S A, 106, 11034-11039.
PDB codes: 3fp6 3fp7 3fp8
19035367 I.Brovchenko, and A.Oleinikova (2008).
Which properties of a spanning network of hydration water enable biological functions?
  Chemphyschem, 9, 2695-2702.  
17553791 J.Lee, A.R.Feldman, B.Delmas, and M.Paetzel (2007).
Crystal structure of the VP4 protease from infectious pancreatic necrosis virus reveals the acyl-enzyme complex for an intermolecular self-cleavage reaction.
  J Biol Chem, 282, 24928-24937.
PDB codes: 2pnl 2pnm
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
16602823 D.A.Kraut, P.A.Sigala, B.Pybus, C.W.Liu, D.Ringe, G.A.Petsko, and D.Herschlag (2006).
Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole.
  PLoS Biol, 4, e99.
PDB codes: 2b32 2pzv
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
16672242 T.T.Baird, W.D.Wright, and C.S.Craik (2006).
Conversion of trypsin to a functional threonine protease.
  Protein Sci, 15, 1229-1238.  
17083959 X.Ding, B.F.Rasmussen, G.A.Petsko, and D.Ringe (2006).
Direct crystallographic observation of an acyl-enzyme intermediate in the elastase-catalyzed hydrolysis of a peptidyl ester substrate: Exploiting the "glass transition" in protein dynamics.
  Bioorg Chem, 34, 410-423.  
15111430 M.Weik, X.Vernede, A.Royant, and D.Bourgeois (2004).
Temperature derivative fluorescence spectroscopy as a tool to study dynamical changes in protein crystals.
  Biophys J, 86, 3176-3185.  
15345526 T.Becker, J.A.Hayward, J.L.Finney, R.M.Daniel, and J.C.Smith (2004).
Neutron frequency windows and the protein dynamical transition.
  Biophys J, 87, 1436-1444.  
12885619 J.A.Hayward, J.L.Finney, R.M.Daniel, and J.C.Smith (2003).
Molecular dynamics decomposition of temperature-dependent elastic neutron scattering by a protein solution.
  Biophys J, 85, 679-685.  
14583255 M.A.McDonough, and C.J.Schofield (2003).
New structural insights into the inhibition of serine proteases by cyclic peptides from bacteria.
  Chem Biol, 10, 898-900.  
12636712 T.Becker, and J.C.Smith (2003).
Energy resolution and dynamical heterogeneity effects on elastic incoherent neutron scattering from molecular systems.
  Phys Rev E Stat Nonlin Soft Matter Phys, 67, 021904.  
12177453 D.J.Heyes, A.V.Ruban, H.M.Wilks, and C.N.Hunter (2002).
Enzymology below 200 K: the kinetics and thermodynamics of the photochemistry catalyzed by protochlorophyllide oxidoreductase.
  Proc Natl Acad Sci U S A, 99, 11145-11150.  
11867439 J.A.Hayward, and J.C.Smith (2002).
Temperature dependence of protein dynamics: computer simulation analysis of neutron scattering properties.
  Biophys J, 82, 1216-1225.  
11420442 N.Ota, and D.A.Agard (2001).
Enzyme specificity under dynamic control II: Principal component analysis of alpha-lytic protease using global and local solvent boundary conditions.
  Protein Sci, 10, 1403-1414.  
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.  
10738204 I.Nakanishi, T.Kinoshita, A.Sato, and T.Tada (2000).
Structure of porcine pancreatic elastase complexed with FR901277, a novel macrocyclic inhibitor of elastases, at 1.6 A resolution.
  Biopolymers, 53, 434-445.
PDB code: 1qr3
10963663 V.Réat, R.Dunn, M.Ferrand, J.L.Finney, R.M.Daniel, and J.C.Smith (2000).
Solvent dependence of dynamic transitions in protein solutions.
  Proc Natl Acad Sci U S A, 97, 9961-9966.  
10328266 S.M.King, and W.C.Johnson (1999).
Assigning secondary structure from protein coordinate data.
  Proteins, 35, 313-320.  
9677373 A.Ordentlich, D.Barak, C.Kronman, N.Ariel, Y.Segall, B.Velan, and A.Shafferman (1998).
Functional characteristics of the oxyanion hole in human acetylcholinesterase.
  J Biol Chem, 273, 19509-19517.  
9636022 J.B.Thoden, S.G.Miran, J.C.Phillips, A.J.Howard, F.M.Raushel, and H.M.Holden (1998).
Carbamoyl phosphate synthetase: caught in the act of glutamine hydrolysis.
  Biochemistry, 37, 8825-8831.
PDB code: 1a9x
9836602 S.R.Presnell, G.S.Patil, C.Mura, K.M.Jude, J.M.Conley, J.A.Bertrand, C.M.Kam, J.C.Powers, and L.D.Williams (1998).
Oxyanion-mediated inhibition of serine proteases.
  Biochemistry, 37, 17068-17081.
PDB codes: 1bju 1bjv
9211842 A.D.Mesecar, B.L.Stoddard, and D.E.Koshland (1997).
Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences.
  Science, 277, 202-206.
PDB codes: 1ai2 1ai3
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
9187653 R.C.Wilmouth, I.J.Clifton, C.V.Robinson, P.L.Roach, R.T.Aplin, N.J.Westwood, J.Hajdu, and C.J.Schofield (1997).
Structure of a specific acyl-enzyme complex formed between beta-casomorphin-7 and porcine pancreatic elastase.
  Nat Struct Biol, 4, 456-462.
PDB code: 1qix
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.  
8574702 K.Moffat, and R.Henderson (1995).
Freeze trapping of reaction intermediates.
  Curr Opin Struct Biol, 5, 656-663.  
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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