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PDBsum entry 5ptp

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Serine protease PDB id
5ptp
Jmol
Contents
Protein chain
223 a.a. *
Metals
_CA
Waters ×211
* Residue conservation analysis
PDB id:
5ptp
Name: Serine protease
Title: Structure of hydrolase (serine proteinase)
Structure: Beta trypsin. Chain: a. Ec: 3.4.21.4
Source: Bos taurus. Cattle. Organism_taxid: 9913
Resolution:
1.34Å     R-factor:   0.152    
Authors: R.M.Stroud,J.Finer-Moore
Key ref: J.S.Finer-Moore et al. (1992). Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction. Proteins, 12, 203-222. PubMed id: 1557349
Date:
31-Mar-97     Release date:   07-Jul-97    
Supersedes: 4ptp
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00760  (TRY1_BOVIN) -  Cationic trypsin
Seq:
Struc:
246 a.a.
223 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.3.4.21.4  - Trypsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     digestion   2 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
Proteins 12:203-222 (1992)
PubMed id: 1557349  
 
 
Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction.
J.S.Finer-Moore, A.A.Kossiakoff, J.H.Hurley, T.Earnest, R.M.Stroud.
 
  ABSTRACT  
 
The solvent structure in orthorhombic crystals of bovine trypsin has been independently determined by X-ray diffraction to 1.35 A resolution and by neutron diffraction to 2.1 A resolution. A consensus model of the water molecule positions was obtained using oxygen positions identified in the electron density map determined by X-ray diffraction, which were verified by comparison to D2O-H2O difference neutron scattering density. Six of 184 water molecules in the X-ray structure, all with B-factors greater than 50 A2, were found to be spurious after comparison with neutron results. Roughly two-thirds of the water of hydration expected from thermodynamic data for proteins was localized by neutron diffraction; approximately one-half of the water of hydration was located by X-ray diffraction. Polar regions of the protein are well hydrated, and significant D2O-H2O difference density is seen for a small number of water molecules in a second shell of hydration. Hydrogen bond lengths and angles calculated from unconstrained refinement of water positions are distributed about values typically seen in small molecule structures. Solvent models found in seven other bovine trypsin and trypsinogen and rat trypsin structures determined by X-ray diffraction were compared. Internal water molecules are well conserved in all trypsin structures including anionic rat trypsin, which is 65% homologous to bovine trypsin. Of the 22 conserved waters in trypsin, 19 were also found in trypsinogen, suggesting that they are located in regions of the apoprotein that are structurally conserved in the transition to the mature protein. Seven waters were displaced upon activation of trypsinogen. Water structure at crystal contacts is not generally conserved in different crystal forms. Three groups of integral structural water molecules are highly conserved in all solvent structures, including a spline of water molecules inserted between two beta-strands, which may resemble an intermediate in the formation of beta sheets during the folding of a protein.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21481775 T.D.Fenn, M.J.Schnieders, M.Mustyakimov, C.Wu, P.Langan, V.S.Pande, and A.T.Brunger (2011).
Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.
  Structure, 19, 523-533.
PDB code: 3qba
18178652 J.L.Schlessman, C.Abe, A.Gittis, D.A.Karp, M.A.Dolan, and B.García-Moreno E (2008).
Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups.
  Biophys J, 94, 3208-3216.
PDB codes: 2pw5 2pw7 2pyk 2pzt 2pzu 2pzw
18060440 T.H.Roberts, and J.Hejgaard (2008).
Serpins in plants and green algae.
  Funct Integr Genomics, 8, 1.  
17397537 S.V.Rakhmanov, and V.J.Makeev (2007).
Atomic hydration potentials using a Monte Carlo Reference State (MCRS) for protein solvation modeling.
  BMC Struct Biol, 7, 19.  
17186526 T.Imai, R.Hiraoka, A.Kovalenko, and F.Hirata (2007).
Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation.
  Proteins, 66, 804-813.  
16287115 S.Bhat, and E.O.Purisima (2006).
Molecular surface generation using a variable-radius solvent probe.
  Proteins, 62, 244-261.  
14747701 L.Prasad, Y.Leduc, K.Hayakawa, and L.T.Delbaere (2004).
The structure of a universally employed enzyme: V8 protease from Staphylococcus aureus.
  Acta Crystallogr D Biol Crystallogr, 60, 256-259.
PDB codes: 1qy6 2o8l
15306376 M.Nakasako (2004).
Water-protein interactions from high-resolution protein crystallography.
  Philos Trans R Soc Lond B Biol Sci, 359, 1191.  
15272158 T.Chatake, K.Kurihara, I.Tanaka, I.Tsyba, R.Bau, F.E.Jenney, M.W.Adams, and N.Niimura (2004).
A neutron crystallographic analysis of a rubredoxin mutant at 1.6 A resolution.
  Acta Crystallogr D Biol Crystallogr, 60, 1364-1373.
PDB codes: 1iu5 1iu6
11927576 J.Funahashi, K.Takano, Y.Yamagata, and K.Yutani (2002).
Positive contribution of hydration structure on the surface of human lysozyme to the conformational stability.
  J Biol Chem, 277, 21792-21800.
PDB codes: 1gf8 1gf9 1gfa 1gfe 1gfg 1gfh 1gfj 1gfk 1gfr 1gft 1gfu 1gfv 1inu
12377789 J.Phan, A.Zdanov, A.G.Evdokimov, J.E.Tropea, H.K.Peters, R.B.Kapust, M.Li, A.Wlodawer, and D.S.Waugh (2002).
Structural basis for the substrate specificity of tobacco etch virus protease.
  J Biol Chem, 277, 50564-50572.
PDB codes: 1lvb 1lvm
11264577 H.K.Leiros, S.M.McSweeney, and A.O.Smalås (2001).
Atomic resolution structures of trypsin provide insight into structural radiation damage.
  Acta Crystallogr D Biol Crystallogr, 57, 488-497.
PDB codes: 1hj8 1hj9
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
10737927 A.Luise, M.Falconi, and A.Desideri (2000).
Molecular dynamics simulation of solvated azurin: correlation between surface solvent accessibility and water residence times.
  Proteins, 39, 56-67.  
10769113 D.H.Kim, D.S.Jang, G.H.Nam, G.Choi, J.S.Kim, N.C.Ha, M.S.Kim, B.H.Oh, and K.Y.Choi (2000).
Contribution of the hydrogen-bond network involving a tyrosine triad in the active site to the structure and function of a highly proficient ketosteroid isomerase from Pseudomonas putida biotype B.
  Biochemistry, 39, 4581-4589.
PDB codes: 1dmm 1dmn 1dmq
10707029 J.D.Szustakowski, and Z.Weng (2000).
Protein structure alignment using a genetic algorithm.
  Proteins, 38, 428-440.  
10656264 S.Dennis, C.J.Camacho, and S.Vajda (2000).
Continuum electrostatic analysis of preferred solvation sites around proteins in solution.
  Proteins, 38, 176-188.  
10450092 C.A.Schiffer, and W.F.van Gunsteren (1999).
Accessibility and order of water sites in and around proteins: A crystallographic time-averaging study.
  Proteins, 36, 501-511.  
10216294 C.Bon, M.S.Lehmann, and C.Wilkinson (1999).
Quasi-Laue neutron-diffraction study of the water arrangement in crystals of triclinic hen egg-white lysozyme.
  Acta Crystallogr D Biol Crystallogr, 55, 978-987.
PDB code: 1lzn
10508767 N.Niimura (1999).
Neutrons expand the field of structural biology.
  Curr Opin Struct Biol, 9, 602-608.  
10089359 O.Carugo, and D.Bordo (1999).
How many water molecules can be detected by protein crystallography?
  Acta Crystallogr D Biol Crystallogr, 55, 479-483.  
17030337 R.Guzzi, C.Arcangeli, and A.R.Bizzarri (1999).
A molecular dynamics simulation study of the solvent isotope effect on copper plastocyanin.
  Biophys Chem, 82, 9.  
  9568894 B.A.Katz, B.Liu, M.Barnes, and E.B.Springman (1998).
Crystal structure of recombinant human tissue kallikrein at 2.0 A resolution.
  Protein Sci, 7, 875-885.  
9443338 M.M.Krem, and E.Di Cera (1998).
Conserved water molecules in the specificity pocket of serine proteases and the molecular mechanism of Na+ binding.
  Proteins, 30, 34-42.  
  9792092 P.C.Sanschagrin, and L.A.Kuhn (1998).
Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity.
  Protein Sci, 7, 2054-2064.  
10076803 V.Boden, M.H.Rangeard, N.Mrabet, and M.A.Vijayalakshmi (1998).
Histidine mapping of serine protease: a synergic study by IMAC and molecular modelling.
  J Mol Recognit, 11, 32-39.  
9148939 B.A.Katz, and R.T.Cass (1997).
In crystals of complexes of streptavidin with peptide ligands containing the HPQ sequence the pKa of the peptide histidine is less than 3.0.
  J Biol Chem, 272, 13220-13228.
PDB codes: 1vwa 1vwb 1vwc 1vwd 1vwe 1vwf 1vwg 1vwh 1vwi 1vwj 1vwk 1vwl 1vwm 1vwn 1vwo 1vwp 1vwq 1vwr
9017183 H.Resat, T.J.Marrone, and J.A.McCammon (1997).
Enzyme-inhibitor association thermodynamics: explicit and continuum solvent studies.
  Biophys J, 72, 522-532.  
9360606 N.Niimura, Y.Minezaki, T.Nonaka, J.C.Castagna, F.Cipriani, P.Høghøj, M.S.Lehmann, and C.Wilkinson (1997).
Neutron Laue diffractometry with an imaging plate provides an effective data collection regime for neutron protein crystallography.
  Nat Struct Biol, 4, 909-914.
PDB code: 1io5
8631340 I.P.Gerothanassis, P.J.Barrie, B.Birdsall, and J.Feeney (1996).
31P solid-state NMR measurements used to detect interactions between NADPH and water and to determine the ionisation state of NADPH in a protein-ligand complex subjected to low-level hydration.
  Eur J Biochem, 235, 262-266.  
8816770 M.Gerstein, and C.Chothia (1996).
Packing at the protein-water interface.
  Proc Natl Acad Sci U S A, 93, 10167-10172.  
9383463 B.A.Katz, R.M.Stroud, N.Collins, B.Liu, and R.Arze (1995).
Topochemistry for preparing ligands that dimerize receptors.
  Chem Biol, 2, 591-600.  
8619952 B.C.Braden, B.A.Fields, and R.J.Poljak (1995).
Conservation of water molecules in an antibody-antigen interaction.
  J Mol Recognit, 8, 317-325.  
8789192 C.S.Poornima, and P.M.Dean (1995).
Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions.
  J Comput Aided Mol Des, 9, 500-512.  
8789193 C.S.Poornima, and P.M.Dean (1995).
Hydration in drug design. 2. Influence of local site surface shape on water binding.
  J Comput Aided Mol Des, 9, 513-520.  
8789194 C.S.Poornima, and P.M.Dean (1995).
Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins.
  J Comput Aided Mol Des, 9, 521-531.  
7781068 G.Zhang, M.G.Kazanietz, P.M.Blumberg, and J.H.Hurley (1995).
Crystal structure of the cys2 activator-binding domain of protein kinase C delta in complex with phorbol ester.
  Cell, 81, 917-924.
PDB codes: 1ptq 1ptr
8749849 L.A.Kuhn, C.A.Swanson, M.E.Pique, J.A.Tainer, and E.D.Getzoff (1995).
Atomic and residue hydrophilicity in the context of folded protein structures.
  Proteins, 23, 536-547.  
  7756979 S.J.Hubbard, and P.Argos (1994).
Cavities and packing at protein interfaces.
  Protein Sci, 3, 2194-2206.  
  7920248 X.J.Zhang, and B.W.Matthews (1994).
Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme.
  Protein Sci, 3, 1031-1039.
PDB codes: 149l 150l 151l 152l
8081736 M.Levitt, and B.H.Park (1993).
Water: now you see it, now you don't.
  Structure, 1, 223-226.  
1557350 A.A.Kossiakoff, M.D.Sintchak, J.Shpungin, and L.G.Presta (1992).
Analysis of solvent structure in proteins using neutron D2O-H2O solvent maps: pattern of primary and secondary hydration of trypsin.
  Proteins, 12, 223-236.  
  1304887 E.Meyer (1992).
Internal water molecules and H-bonding in biological macromolecules: a review of structural features with functional implications.
  Protein Sci, 1, 1543-1562.  
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.