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PDBsum entry 3est
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Hydrolase(serine proteinase) PDB id
3est

 

 

 

 

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Contents
Protein chain
240 a.a. *
Ligands
SO4 ×2
Metals
_CA
Waters ×127
* Residue conservation analysis
PDB id:
3est
Name: Hydrolase(serine proteinase)
Title: Structure of native porcine pancreatic elastase at 1.65 angstroms resolution
Structure: Porcine pancreatic elastase. Chain: a. Engineered: yes
Source: Sus scrofa. Pig. Organism_taxid: 9823
Resolution:
1.65Å     R-factor:   0.169    
Authors: E.F.Meyer,G.Cole,R.Radhakrishnan,O.Epp
Key ref: E.Meyer et al. (1988). Structure of native porcine pancreatic elastase at 1.65 A resolutions. Acta Crystallogr B, 44, 26-38. PubMed id: 3271103
Date:
17-Sep-87     Release date:   16-Jan-88    
PROCHECK
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 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.

 

 
Acta Crystallogr B 44:26-38 (1988)
PubMed id: 3271103  
 
 
Structure of native porcine pancreatic elastase at 1.65 A resolutions.
E.Meyer, G.Cole, R.Radhakrishnan, O.Epp.
 
  ABSTRACT  
 
The structure of native porcine pancreatic elastase in 70% methanol has been refined using film data to 1.65 A resolution, R = 0.169. A total of 134 molecules of water (but no methanol) has been refined. This structure, because of its native state and modestly high resolution, serves as the basis for comparison with other elastase structures complexed with natural or synthetic ligands. Internal structured water occupies distinct regions. Two regions (IW1 and IW7) suggest a mechanism for equalizing 'hydrostatic pressure' related to ligand binding and release. A third region (IW4) forms part of a hydrogen-bonding network linking the catalytic Ser 195 O gamma with a remote (13.4 A) surface of the enzyme. A comparison with the structures of all known serine proteases reveals that a linkage of Ser O gamma to remote surface is conserved in all cases, suggesting that the accepted catalytic mechanism of serine proteases needs to be re-evaluated. One possible mechanism for base catalysis of Ser O gamma H proton extraction is presented.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19937325 R.C.Cheng, and B.S.Zhorov (2010).
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1.70 A X-ray structure of human apo kallikrein 1: structural changes upon peptide inhibitor/substrate binding.
  Proteins, 58, 802-814.
PDB code: 1spj
16021597 R.Villar, M.J.Gil, J.I.García, and V.Martínez-Merino (2005).
Are AM1 ligand-protein binding enthalpies good enough for use in the rational design of new drugs?
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11358514 P.A.Wright, R.C.Wilmouth, I.J.Clifton, and C.J.Schofield (2001).
Kinetic and crystallographic analysis of complexes formed between elastase and peptides from beta-casein.
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PDB code: 1h9l
11526210 Y.Liu, C.M.Ogata, and W.A.Hendrickson (2001).
Multiwavelength anomalous diffraction analysis at the M absorption edges of uranium.
  Proc Natl Acad Sci U S A, 98, 10648-10653.  
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Crystal structure of recombinant human tissue kallikrein at 2.0 A resolution.
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The functions of the first epidermal growth factor homology region of human protein C as revealed by a charge-to-alanine scanning mutagenesis investigation.
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  9232643 D.E.Timm (1997).
The crystal structure of the mouse glandular kallikrein-13 (prorenin converting enzyme).
  Protein Sci, 6, 1418-1425.
PDB code: 1ao5
  7556081 F.X.Gomis-Rüth, M.Gómez, W.Bode, R.Huber, and F.X.Avilés (1995).
The three-dimensional structure of the native ternary complex of bovine pancreatic procarboxypeptidase A with proproteinase E and chymotrypsinogen C.
  EMBO J, 14, 4387-4394.
PDB code: 1pyt
7788296 M.Schiltz, R.Fourme, I.Broutin, and T.Prangé (1995).
The catalytic site of serine proteinases as a specific binding cavity for xenon.
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  7756993 A.A.Adzhubei, and M.J.Sternberg (1994).
Conservation of polyproline II helices in homologous proteins: implications for structure prediction by model building.
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  8168476 D.Pignol, C.Gaboriaud, T.Michon, B.Kerfelec, C.Chapus, and J.C.Fontecilla-Camps (1994).
Crystal structure of bovine procarboxypeptidase A-S6 subunit III, a highly structured truncated zymogen E.
  EMBO J, 13, 1763-1771.
PDB code: 1fon
8302861 E.Pizzi, A.Tramontano, L.Tomei, N.La Monica, C.Failla, M.Sardana, T.Wood, and R.De Francesco (1994).
Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition.
  Proc Natl Acad Sci U S A, 91, 888-892.  
7922044 K.Huang, N.C.Strynadka, V.D.Bernard, R.J.Peanasky, and M.N.James (1994).
The molecular structure of the complex of Ascaris chymotrypsin/elastase inhibitor with porcine elastase.
  Structure, 2, 679-689.
PDB code: 1eai
  7756992 L.E.Donate, E.Gherardi, N.Srinivasan, R.Sowdhamini, S.Aparicio, and T.L.Blundell (1994).
Molecular evolution and domain structure of plasminogen-related growth factors (HGF/SF and HGF1/MSP).
  Protein Sci, 3, 2378-2394.  
  7987217 M.A.Williams, J.M.Goodfellow, and J.M.Thornton (1994).
Buried waters and internal cavities in monomeric proteins.
  Protein Sci, 3, 1224-1235.  
  8156987 M.E.McGrath, T.Erpel, C.Bystroff, and R.J.Fletterick (1994).
Macromolecular chelation as an improved mechanism of protease inhibition: structure of the ecotin-trypsin complex.
  EMBO J, 13, 1502-1507.  
8035212 S.D.Rufino, and T.L.Blundell (1994).
Structure-based identification and clustering of protein families and superfamilies.
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7803238 T.Miyata, K.Kuze, T.Matsusue, H.Komooka, K.Kamiya, H.Umeyama, A.Matsui, H.Kato, and A.Yoshioka (1994).
Factor IX Bm Kiryu: a Val-313-to-Asp substitution in the catalytic domain results in loss of function due to a conformational change of the surface loop: evidence obtained by chimaeric modelling.
  Br J Haematol, 88, 156-165.  
7681210 A.S.Yang, M.R.Gunner, R.Sampogna, K.Sharp, and B.Honig (1993).
On the calculation of pKas in proteins.
  Proteins, 15, 252-265.  
8475107 C.S.Ring, E.Sun, J.H.McKerrow, G.K.Lee, P.J.Rosenthal, I.D.Kuntz, and F.E.Cohen (1993).
Structure-based inhibitor design by using protein models for the development of antiparasitic agents.
  Proc Natl Acad Sci U S A, 90, 3583-3587.  
8436108 J.L.Martini, C.Tetreau, F.Pochon, H.Tourbez, J.M.Lentz, and D.Lavalette (1993).
On the mechanism of energy transfer to Tb3+ ions in proteins. A time-resolved luminescence study of the Tb-elastase complex.
  Eur J Biochem, 211, 467-473.  
  1304349 W.Bode, D.Turk, and A.Karshikov (1992).
The refined 1.9-A X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human alpha-thrombin: structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships.
  Protein Sci, 1, 426-471.
PDB codes: 1ai8 1aix
2017436 C.Sander, and R.Schneider (1991).
Database of homology-derived protein structures and the structural meaning of sequence alignment.
  Proteins, 9, 56-68.  
1799460 P.Ascenzi, P.Aducci, G.Amiconi, A.Ballio, A.Guaragna, E.Menegatti, H.P.Schnebli, and M.Bolognesi (1991).
Binding of the recombinant proteinase inhibitor eglin c from leech Hirudo medicinalis to serine (pro)enzymes: a comparative thermodynamic study.
  J Mol Recognit, 4, 113-119.  
2352930 A.A.Kossiakoff, J.Shpungin, and M.D.Sintchak (1990).
Hydroxyl hydrogen conformations in trypsin determined by the neutron diffraction solvent difference map method: relative importance of steric and electrostatic factors in defining hydrogen-bonding geometries.
  Proc Natl Acad Sci U S A, 87, 4468-4472.  
2107323 M.S.Johnson, M.J.Sutcliffe, and T.L.Blundell (1990).
Molecular anatomy: phyletic relationships derived from three-dimensional structures of proteins.
  J Mol Evol, 30, 43-59.  
  2583108 W.Bode, I.Mayr, U.Baumann, R.Huber, S.R.Stone, and J.Hofsteenge (1989).
The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment.
  EMBO J, 8, 3467-3475.
PDB code: 1ppb
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.

 

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