spacer
spacer

PDBsum entry 1lz1

Go to PDB code: 
protein links
Hydrolase (o-glycosyl) PDB id
1lz1
Jmol PyMol
Contents
Protein chain
130 a.a. *
* Residue conservation analysis
PDB id:
1lz1
Name: Hydrolase (o-glycosyl)
Title: Refinement of human lysozyme at 1.5 angstroms resolution. Analysis of non-bonded and hydrogen-bond interactions
Structure: Human lysozyme. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
Resolution:
1.50Å     R-factor:   0.177    
Authors: P.J.Artymiuk,C.C.F.Blake
Key ref:
P.J.Artymiuk and C.C.Blake (1981). Refinement of human lysozyme at 1.5 A resolution analysis of non-bonded and hydrogen-bond interactions. J Mol Biol, 152, 737-762. PubMed id: 7334520 DOI: 10.1016/0022-2836(81)90125-X
Date:
12-Oct-84     Release date:   02-Jan-85    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P61626  (LYSC_HUMAN) -  Lysozyme C
Seq:
Struc:
148 a.a.
130 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.17  - 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     extracellular region   6 terms 
  Biological process     metabolic process   8 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
DOI no: 10.1016/0022-2836(81)90125-X J Mol Biol 152:737-762 (1981)
PubMed id: 7334520  
 
 
Refinement of human lysozyme at 1.5 A resolution analysis of non-bonded and hydrogen-bond interactions.
P.J.Artymiuk, C.C.Blake.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 10.
FIG. 10. Histograms of H&O ngles (a) for NH-O distances < 2.5 A.
Figure 11.
FIG. 11. Definition of the hydrogen bond angles fl and y at the accptor oxygen
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1981, 152, 737-762) copyright 1981.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21354256 N.Sarkar, M.Kumar, and V.K.Dubey (2011).
Effect of sodium tetrathionate on amyloid fibril: Insight into the role of disulfide bond in amyloid progression.
  Biochimie, 93, 962-968.  
20958028 A.Dhulesia, N.Cremades, J.R.Kumita, S.T.Hsu, M.F.Mossuto, M.Dumoulin, D.Nietlispach, M.Akke, X.Salvatella, and C.M.Dobson (2010).
Local cooperativity in an amyloidogenic state of human lysozyme observed at atomic resolution.
  J Am Chem Soc, 132, 15580-15588.  
20382744 C.L.Hagan, R.J.Johnson, A.Dhulesia, M.Dumoulin, J.Dumont, E.De Genst, J.Christodoulou, C.V.Robinson, C.M.Dobson, and J.R.Kumita (2010).
A non-natural variant of human lysozyme (I59T) mimics the in vitro behaviour of the I56T variant that is responsible for a form of familial amyloidosis.
  Protein Eng Des Sel, 23, 499-506.  
19307716 J.A.Doebbler, and R.B.Von Dreele (2009).
Application of molecular replacement to protein powder data from image plates.
  Acta Crystallogr D Biol Crystallogr, 65, 348-355.  
19348005 Y.Nonaka, D.Akieda, T.Aizawa, N.Watanabe, M.Kamiya, Y.Kumaki, M.Mizuguchi, T.Kikukawa, M.Demura, and K.Kawano (2009).
X-ray crystallography and structural stability of digestive lysozyme from cow stomach.
  FEBS J, 276, 2192-2200.  
  19164912 M.T.Pastor, A.Esteras-Chopo, and L.Serrano (2007).
Hacking the code of amyloid formation: the amyloid stretch hypothesis.
  Prion, 1, 9.  
16441658 J.R.Kumita, R.J.Johnson, M.J.Alcocer, M.Dumoulin, F.Holmqvist, M.G.McCammon, C.V.Robinson, D.B.Archer, and C.M.Dobson (2006).
Impact of the native-state stability of human lysozyme variants on protein secretion by Pichia pastoris.
  FEBS J, 273, 711-720.  
16231289 H.Li, A.D.Robertson, and J.H.Jensen (2005).
Very fast empirical prediction and rationalization of protein pKa values.
  Proteins, 61, 704-721.  
14997542 H.Kaur, and G.P.Raghava (2004).
Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information.
  Proteins, 55, 83-90.  
15280548 R.S.Armen, M.L.DeMarco, D.O.Alonso, and V.Daggett (2004).
Pauling and Corey's alpha-pleated sheet structure may define the prefibrillar amyloidogenic intermediate in amyloid disease.
  Proc Natl Acad Sci U S A, 101, 11622-11627.  
12668424 G.Moraitakis, and J.M.Goodfellow (2003).
Simulations of human lysozyme: probing the conformations triggering amyloidosis.
  Biophys J, 84, 2149-2158.  
12919320 M.Stuart-Audette, Y.Blouquit, M.Faraggi, C.Sicard-Roselli, C.Houée-Levin, and P.Jollès (2003).
Re-evaluation of intramolecular long-range electron transfer between tyrosine and tryptophan in lysozymes. Evidence for the participation of other residues.
  Eur J Biochem, 270, 3565-3571.  
11847273 M.Dumoulin, K.Conrath, A.Van Meirhaeghe, F.Meersman, K.Heremans, L.G.Frenken, S.Muyldermans, L.Wyns, and A.Matagne (2002).
Single-domain antibody fragments with high conformational stability.
  Protein Sci, 11, 500-515.  
10873859 A.D.Ferguson, W.Welte, E.Hofmann, B.Lindner, O.Holst, J.W.Coulton, and K.Diederichs (2000).
A conserved structural motif for lipopolysaccharide recognition by procaryotic and eucaryotic proteins.
  Structure, 8, 585-592.
PDB codes: 1qff 1qfg
10913274 K.Takano, Y.Yamagata, and K.Yutani (2000).
Role of amino acid residues at turns in the conformational stability and folding of human lysozyme.
  Biochemistry, 39, 8655-8665.
PDB codes: 1di3 1di4 1di5 1gaz
10727242 M.Arai, P.Hamel, E.Kanaya, K.Inaka, K.Miki, M.Kikuchi, and K.Kuwajima (2000).
Effect of an alternative disulfide bond on the structure, stability, and folding of human lysozyme.
  Biochemistry, 39, 3472-3479.  
  10716189 S.Goda, K.Takano, Y.Yamagata, R.Nagata, H.Akutsu, S.Maki, K.Namba, and K.Yutani (2000).
Amyloid protofilament formation of hen egg lysozyme in highly concentrated ethanol solution.
  Protein Sci, 9, 369-375.  
  11045614 S.Mine, T.Ueda, Y.Hashimoto, and T.Imoto (2000).
Analysis of the internal motion of free and ligand-bound human lysozyme by use of 15N NMR relaxation measurement: a comparison with those of hen lysozyme.
  Protein Sci, 9, 1669-1684.  
10727216 T.Koshiba, M.Yao, Y.Kobashigawa, M.Demura, A.Nakagawa, I.Tanaka, K.Kuwajima, and K.Nitta (2000).
Structure and thermodynamics of the extraordinarily stable molten globule state of canine milk lysozyme.
  Biochemistry, 39, 3248-3257.
PDB code: 1qqy
10679617 V.Tsikaris, A.Troganis, V.Moussis, E.Panou-Pomonis, M.Sakarellos-Daitsiotis, and C.Sakarellos (2000).
Arg side-chain-backbone interactions evidenced in model peptides by 17O-NMR spectroscopy.
  Biopolymers, 53, 135-139.  
10635562 C.Oka, M.Tanaka, M.Muraki, K.Harata, K.Suzuki, and Y.Jigami (1999).
Human lysozyme secretion increased by alpha-factor pro-sequence in Pichia pastoris.
  Biosci Biotechnol Biochem, 63, 1977-1983.  
10226504 D.S.Dwyer (1999).
Molecular simulation of the effects of alcohols on peptide structure.
  Biopolymers, 49, 635-645.  
9888793 M.Muraki, K.Harata, N.Sugita, and K.Sato (1999).
Dual affinity labeling of the active site of human lysozyme with an N-acetyllactosamine derivative: first ligand assisted recognition of the second ligand.
  Biochemistry, 38, 540-548.
PDB code: 1re2
9852096 R.Kuroki, and K.Yutani (1998).
Structural and thermodynamic responses of mutations at a Ca2+ binding site engineered into human lysozyme.
  J Biol Chem, 273, 34310-34315.
PDB codes: 1i1z 1i20 1i22
9649316 Y.Yamagata, M.Kubota, Y.Sumikawa, J.Funahashi, K.Takano, S.Fujii, and K.Yutani (1998).
Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six tyrosine --> phenylalanine mutants.
  Biochemistry, 37, 9355-9362.
PDB codes: 1wqm 1wqn 1wqo 1wqp 1wqq 1wqr
  9041653 M.Muraki, S.Goda, H.Nagahora, and K.Harata (1997).
Importance of van der Waals contact between Glu 35 and Trp 109 to the catalytic action of human lysozyme.
  Protein Sci, 6, 473-476.
PDB codes: 1jka 1jkb 1jkc 1jkd
8805552 A.C.Pike, K.Brew, and K.R.Acharya (1996).
Crystal structures of guinea-pig, goat and bovine alpha-lactalbumin highlight the enhanced conformational flexibility of regions that are significant for its action in lactose synthase.
  Structure, 4, 691-703.
PDB codes: 1hfx 1hfy 1hfz
8885835 M.Muraki, K.Harata, N.Sugita, and K.Sato (1996).
Origin of carbohydrate recognition specificity of human lysozyme revealed by affinity labeling.
  Biochemistry, 35, 13562-13567.
PDB codes: 1rex 1rey 1rez
8652792 V.Pavone, G.Gaeta, A.Lombardi, F.Nastri, O.Maglio, C.Isernia, and M.Saviano (1996).
Discovering protein secondary structures: classification and description of isolated alpha-turns.
  Biopolymers, 38, 705-721.  
8749853 D.Frishman, and P.Argos (1995).
Knowledge-based protein secondary structure assignment.
  Proteins, 23, 566-579.  
7737986 E.Pardon, P.Haezebrouck, A.De Baetselier, S.D.Hooke, K.T.Fancourt, J.Desmet, C.M.Dobson, H.Van Dael, and M.Joniau (1995).
A Ca(2+)-binding chimera of human lysozyme and bovine alpha-lactalbumin that can form a molten globule.
  J Biol Chem, 270, 10514-10524.  
7708754 K.R.Acharya, R.Shapiro, J.F.Riordan, and B.L.Vallee (1995).
Crystal structure of bovine angiogenin at 1.5-A resolution.
  Proc Natl Acad Sci U S A, 92, 2949-2953.
PDB code: 1agi
  8535242 P.Shih, and J.F.Kirsch (1995).
Design and structural analysis of an engineered thermostable chicken lysozyme.
  Protein Sci, 4, 2063-2072.  
8747434 S.Gohda, A.Shimizu, M.Ikeguchi, and S.Sugai (1995).
The superreactive disulfide bonds in alpha-lactalbumin and lysozyme.
  J Protein Chem, 14, 731-737.  
  8003972 C.L.Borders, J.A.Broadwater, P.A.Bekeny, J.E.Salmon, A.S.Lee, A.M.Eldridge, and V.B.Pett (1994).
A structural role for arginine in proteins: multiple hydrogen bonds to backbone carbonyl oxygens.
  Protein Sci, 3, 541-548.  
  7756980 E.G.Hutchinson, and J.M.Thornton (1994).
A revised set of potentials for beta-turn formation in proteins.
  Protein Sci, 3, 2207-2216.  
7832986 K.R.Acharya, D.I.Stuart, D.C.Phillips, H.A.McKenzie, and C.G.Teahan (1994).
Models of the three-dimensional structures of echidna, horse, and pigeon lysozymes: calcium-binding lysozymes and their relationship with alpha-lactalbumins.
  J Protein Chem, 13, 569-584.  
8159663 V.Lounnas, and B.M.Pettitt (1994).
A connected-cluster of hydration around myoglobin: correlation between molecular dynamics simulations and experiment.
  Proteins, 18, 133-147.  
8497485 E.Cheah, G.W.Ashley, J.Gary, and D.Ollis (1993).
Catalysis by dienelactone hydrolase: a variation on the protease mechanism.
  Proteins, 16, 64-78.  
8441751 R.P.Kosman, J.E.Gouaux, and W.N.Lipscomb (1993).
Crystal structure of CTP-ligated T state aspartate transcarbamoylase at 2.5 A resolution: implications for ATCase mutants and the mechanism of negative cooperativity.
  Proteins, 15, 147-176.
PDB codes: 1raa 1rab 1rac 1rad 1rae 1raf 1rag 1rah 1rai
8099449 T.Keitel, O.Simon, R.Borriss, and U.Heinemann (1993).
Molecular and active-site structure of a Bacillus 1,3-1,4-beta-glucanase.
  Proc Natl Acad Sci U S A, 90, 5287-5291.
PDB code: 1byh
  1363898 K.Harata, M.Muraki, Y.Hayashi, and Y.Jigami (1992).
X-ray structure of Glu 53 human lysozyme.
  Protein Sci, 1, 1447-1453.
PDB code: 1laa
1420975 T.Takahashi, H.Nakamura, and A.Wada (1992).
Electrostatic forces in two lysozymes: calculations and measurements of histidine pKa values.
  Biopolymers, 32, 897-909.  
1866431 D.Pathak, G.Ashley, and D.Ollis (1991).
Thiol protease-like active site found in the enzyme dienelactone hydrolase: localization using biochemical, genetic, and structural tools.
  Proteins, 9, 267-279.  
1907667 J.Rose, and F.Eisenmenger (1991).
A fast unbiased comparison of protein structures by means of the Needleman-Wunsch algorithm.
  J Mol Evol, 32, 340-354.  
1896424 T.Horiuchi, and N.Go (1991).
Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: human lysozyme.
  Proteins, 10, 106-116.  
1765071 Y.J.Zhao, E.Sulkowski, and J.Porath (1991).
Surface topography of histidine residues in lysozymes.
  Eur J Biochem, 202, 1115-1119.  
2281087 J.F.Gibrat, and N.Go (1990).
Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion.
  Proteins, 8, 258-279.  
2235992 M.M.Teeter, X.Q.Ma, U.Rao, and M.Whitlow (1990).
Crystal structure of a protein-toxin alpha 1-purothionin at 2.5A and a comparison with predicted models.
  Proteins, 8, 118-132.  
2166604 M.Nilges, G.M.Clore, and A.M.Gronenborn (1990).
1H-NMR stereospecific assignments by conformational data-base searches.
  Biopolymers, 29, 813-822.  
2664781 D.P.Sun, D.I.Liao, and S.J.Remington (1989).
Electrostatic fields in the active sites of lysozymes.
  Proc Natl Acad Sci U S A, 86, 5361-5365.  
2493374 M.Muraki, M.Morikawa, Y.Jigami, and H.Tanaka (1989).
A structural requirement in the subsite F of lysozyme. The role of arginine 115 in human lysozyme revealed by site-directed mutagenesis.
  Eur J Biochem, 179, 573-579.  
2674939 R.Kuroki, Y.Taniyama, C.Seko, H.Nakamura, M.Kikuchi, and M.Ikehara (1989).
Design and creation of a Ca2+ binding site in human lysozyme to enhance structural stability.
  Proc Natl Acad Sci U S A, 86, 6903-6907.  
3059346 M.Kikuchi, Y.Yamamoto, Y.Taniyama, K.Ishimaru, W.Yoshikawa, Y.Kaisho, and M.Ikehara (1988).
Secretion in yeast of human lysozymes with different specific activities created by replacing valine-110 with proline by site-directed mutagenesis.
  Proc Natl Acad Sci U S A, 85, 9411-9415.  
3186702 T.O.Yeates, H.Komiya, A.Chirino, D.C.Rees, J.P.Allen, and G.Feher (1988).
Structure of the reaction center from Rhodobacter sphaeroides R-26 and 2.4.1: protein-cofactor (bacteriochlorophyll, bacteriopheophytin, and carotenoid) interactions.
  Proc Natl Acad Sci U S A, 85, 7993-7997.
PDB code: 4rcr
3303031 J.P.Priestle, M.G.Grütter, J.L.White, M.G.Vincent, M.Kania, E.Wilson, T.S.Jardetzky, K.Kirschner, and J.N.Jansonius (1987).
Three-dimensional structure of the bifunctional enzyme N-(5'-phosphoribosyl)anthranilate isomerase-indole-3-glycerol-phosphate synthase from Escherichia coli.
  Proc Natl Acad Sci U S A, 84, 5690-5694.  
2431905 B.W.Low, and P.W.Corfield (1986).
Erabutoxin b. Structure/function relationships following initial protein refinement at 0.140-nm resolution.
  Eur J Biochem, 161, 579-587.  
  3709526 C.Chothia, and A.M.Lesk (1986).
The relation between the divergence of sequence and structure in proteins.
  EMBO J, 5, 823-826.  
2417241 J.Novotný, M.Handschumacher, E.Haber, R.E.Bruccoleri, W.B.Carlson, D.W.Fanning, J.A.Smith, and G.D.Rose (1986).
Antigenic determinants in proteins coincide with surface regions accessible to large probes (antibody domains).
  Proc Natl Acad Sci U S A, 83, 226-230.  
3779015 T.Ichiye, B.D.Olafson, S.Swaminathan, and M.Karplus (1986).
Structure and internal mobility of proteins: a molecular dynamics study of hen egg white lysozyme.
  Biopolymers, 25, 1909-1937.  
4076183 J.Boyd, C.M.Dobson, and C.Redfield (1985).
Assignment of resonances in the 1H NMR spectrum of human lysozyme.
  Eur J Biochem, 153, 383-396.  
  2410255 M.J.Darsley, and A.R.Rees (1985).
Three distinct epitopes within the loop region of hen egg lysozyme defined with monoclonal antibodies.
  EMBO J, 4, 383-392.  
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.

 

spacer

spacer