PDBsum entry 151l

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Hydrolase(o-glycosyl) PDB id
Protein chain
162 a.a. *
Waters ×37
* Residue conservation analysis
PDB id:
Name: Hydrolase(o-glycosyl)
Title: Conservation of solvent-binding sites in 10 crystal forms of t4 lysozyme
Structure: T4 lysozyme. Chain: a. Engineered: yes
Source: Enterobacteria phage t4. Organism_taxid: 10665.
Biol. unit: Trimer (from PQS)
2.20Å     R-factor:   0.187    
Authors: X.-J.Zhang,B.W.Matthews
Key ref: 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. PubMed id: 7920248 DOI: 10.1002/pro.5560030705
25-Jan-94     Release date:   30-Apr-94    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00720  (LYS_BPT4) -  Endolysin
164 a.a.
162 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Lysozyme.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     host cell cytoplasm   1 term 
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     4 terms  


DOI no: 10.1002/pro.5560030705 Protein Sci 3:1031-1039 (1994)
PubMed id: 7920248  
Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme.
X.J.Zhang, B.W.Matthews.
Solvent-binding sites were compared in 10 different crystal forms of phage T4 lysozyme that were refined using data from 2.6 A to 1.7 A resolution. The sample included 18 crystallographically independent lysozyme molecules. Despite different crystallization conditions, variable crystal contacts, changes due to mutation, and varying attention to solvent during crystallographic refinement, 62% of the 20 most frequently occupied sites were conserved. Allowing for potential steric interference from neighboring molecules in the crystal lattice, this fraction increased to 79% of the sites. There was, however, no solvent-binding site that was occupied in all 18 lysozyme molecules. A buried double site was occupied in 17 instances and 2 other internal sites were occupied 15 times. Apart from these buried sites, the most frequently occupied sites were often at the amino-termini of alpha-helices. Solvent molecules at the most conserved sites tended to have crystallographic thermal factors lower than average, but atoms with low B-factors were not restricted to these sites. Although superficial inspection may suggest that only 50-60% (or less) of solvent-binding sites are conserved in different crystal forms of a protein, it appears that many sites appear to be empty either because of steric interference or because the apparent occupancy of a given site can vary from crystal to crystal. The X-ray method of identifying sites is somewhat subjective and tends to result in specification only of those solvent molecules that are well ordered and bound with high occupancy, even though there is clear evidence for solvent bound at many additional sites.(ABSTRACT TRUNCATED AT 250 WORDS)

Literature references that cite this PDB file's key reference

  PubMed id Reference
20668762 R.M.Esquerra, I.López-Peña, P.Tipgunlakant, I.Birukou, R.L.Nguyen, J.Soman, J.S.Olson, D.S.Kliger, and R.A.Goldbeck (2010).
Kinetic spectroscopy of heme hydration and ligand binding in myoglobin and isolated hemoglobin chains: an optical window into heme pocket water dynamics.
  Phys Chem Chem Phys, 12, 10270-10278.  
  20636062 A.M.Hawkridge, and D.C.Muddiman (2009).
Mass spectrometry-based biomarker discovery: toward a global proteome index of individuality.
  Annu Rev Anal Chem (Palo Alto Calif), 2, 265-277.  
19655795 R.A.Goldbeck, M.L.Pillsbury, R.A.Jensen, J.L.Mendoza, R.L.Nguyen, J.S.Olson, J.Soman, D.S.Kliger, and R.M.Esquerra (2009).
Optical detection of disordered water within a protein cavity.
  J Am Chem Soc, 131, 12265-12272.
PDB codes: 3h57 3h58
19575413 Y.Wine, N.Cohen-Hadar, R.Lamed, A.Freeman, and F.Frolow (2009).
Modification of protein crystal packing by systematic mutations of surface residues: implications on biotemplating and crystal porosity.
  Biotechnol Bioeng, 104, 444-457.  
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
18816066 N.Ando, B.Barstow, W.A.Baase, A.Fields, B.W.Matthews, and S.M.Gruner (2008).
Structural and thermodynamic characterization of T4 lysozyme mutants and the contribution of internal cavities to pressure denaturation.
  Biochemistry, 47, 11097-11109.  
17604315 A.Damjanović, J.L.Schlessman, C.A.Fitch, A.E.García, and B.García-Moreno E (2007).
Role of flexibility and polarity as determinants of the hydration of internal cavities and pockets in proteins.
  Biophys J, 93, 2791-2804.  
17586772 H.Yamada, T.Tamada, M.Kosaka, K.Miyata, S.Fujiki, M.Tano, M.Moriya, M.Yamanishi, E.Honjo, H.Tada, T.Ino, H.Yamaguchi, J.Futami, M.Seno, T.Nomoto, T.Hirata, M.Yoshimura, and R.Kuroki (2007).
'Crystal lattice engineering,' an approach to engineer protein crystal contacts by creating intermolecular symmetry: crystallization and structure determination of a mutant human RNase 1 with a hydrophobic interface of leucines.
  Protein Sci, 16, 1389-1397.
PDB codes: 2e0j 2e0l 2e0m 2e0o
  17329805 J.R.Hobbs, S.D.Munger, and G.L.Conn (2007).
Monellin (MNEI) at 1.15 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 162-167.
PDB code: 2o9u
16899489 A.D.van Dijk, and A.M.Bonvin (2006).
Solvated docking: introducing water into the modelling of biomolecular complexes.
  Bioinformatics, 22, 2340-2347.  
16844975 K.Sumathi, P.Ananthalakshmi, M.N.Roshan, and K.Sekar (2006).
3dSS: 3D structural superposition.
  Nucleic Acids Res, 34, W128-W132.  
17139088 U.D.Ramirez, and D.M.Freymann (2006).
Analysis of protein hydration in ultrahigh-resolution structures of the SRP GTPase Ffh.
  Acta Crystallogr D Biol Crystallogr, 62, 1520-1534.
PDB codes: 2j45 2j46
15941387 V.Guillemard, H.N.Nedev, A.Berezov, R.Murali, and H.U.Saragovi (2005).
HER2-mediated internalization of a targeted prodrug cytotoxic conjugate is dependent on the valency of the targeting ligand.
  DNA Cell Biol, 24, 350-358.  
15146489 B.S.Sanjeev, and S.Vishveshwara (2004).
Protein-water interactions in ribonuclease A and angiogenin: a molecular dynamics study.
  Proteins, 55, 915-923.  
12756610 A.T.García-Sosa, R.L.Mancera, and P.M.Dean (2003).
WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes.
  J Mol Model, 9, 172-182.  
11807249 B.V.Prasad, and K.Suguna (2002).
Role of water molecules in the structure and function of aspartic proteinases.
  Acta Crystallogr D Biol Crystallogr, 58, 250-259.  
11943548 C.Mattos (2002).
Protein-water interactions in a dynamic world.
  Trends Biochem Sci, 27, 203-208.  
12005435 M.Prabu-Jeyabalan, E.Nalivaika, and C.A.Schiffer (2002).
Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes.
  Structure, 10, 369-381.
PDB codes: 1kj4 1kj7 1kjf 1kjg 1kjh
11468361 G.Pujadas, and J.Palau (2001).
Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site.
  Protein Sci, 10, 1645-1657.  
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.  
  10752611 V.A.Likić, N.Juranić, S.Macura, and F.G.Prendergast (2000).
A "structural" water molecule in the family of fatty acid binding proteins.
  Protein Sci, 9, 497-504.  
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.  
10398928 D.Ringe, and C.Mattos (1999).
Analysis of the binding surfaces of proteins.
  Med Res Rev, 19, 321-331.  
10373011 R.Loris, U.Langhorst, S.De Vos, K.Decanniere, J.Bouckaert, D.Maes, T.R.Transue, and J.Steyaert (1999).
Conserved water molecules in a large family of microbial ribonucleases.
  Proteins, 36, 117-134.
PDB codes: 1bu4 2bu4 3bu4 4bu4 5bu4
9482860 C.R.Robinson, and S.G.Sligar (1998).
Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease.
  Proc Natl Acad Sci U S A, 95, 2186-2191.  
  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.  
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
  9260280 F.Catanzano, G.Graziano, S.Capasso, and G.Barone (1997).
Thermodynamic analysis of the effect of selective monodeamidation at asparagine 67 in ribonuclease A.
  Protein Sci, 6, 1682-1693.  
9630949 C.Mattos, and D.Ringe (1996).
Locating and characterizing binding sites on proteins.
  Nat Biotechnol, 14, 595-599.  
  8897613 C.R.Robinson, and S.G.Sligar (1996).
Participation of water in Hin recombinase--DNA recognition.
  Protein Sci, 5, 2119-2124.  
8889177 J.K.Myers, and C.N.Pace (1996).
Hydrogen bonding stabilizes globular proteins.
  Biophys J, 71, 2033-2039.  
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.  
8539241 C.H.Faerman, and P.A.Karplus (1995).
Consensus preferred hydration sites in six FKBP12-drug complexes.
  Proteins, 23, 1.  
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.  
8749372 D.Ringe (1995).
What makes a binding site a binding site?
  Curr Opin Struct Biol, 5, 825-829.  
7542034 G.Hummer, A.E.García, and D.M.Soumpasis (1995).
Hydration of nucleic acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes.
  Biophys J, 68, 1639-1652.  
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.  
  8535241 P.Shih, D.R.Holland, and J.F.Kirsch (1995).
Thermal stability determinants of chicken egg-white lysozyme core mutants: hydrophobicity, packing volume, and conserved buried water molecules.
  Protein Sci, 4, 2050-2062.
PDB codes: 1lsm 1lsn
7579646 S.J.Hubbard, and P.Argos (1995).
Evidence on close packing and cavities in proteins.
  Curr Opin Biotechnol, 6, 375-381.  
  7833808 M.J.Bennett, and D.Eisenberg (1994).
Refined structure of monomeric diphtheria toxin at 2.3 A resolution.
  Protein Sci, 3, 1464-1475.
PDB code: 1mdt
  7833807 M.J.Bennett, S.Choe, and D.Eisenberg (1994).
Refined structure of dimeric diphtheria toxin at 2.0 A resolution.
  Protein Sci, 3, 1444-1463.
PDB code: 1ddt
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