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PDBsum entry 132l

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Hydrolase(o-glycosyl) PDB id
132l
Jmol
Contents
Protein chain
129 a.a. *
Waters ×78
* Residue conservation analysis
PDB id:
132l
Name: Hydrolase(o-glycosyl)
Title: Structural consequences of reductive methylation of lysine residues in hen egg white lysozyme: an x-ray analysis at 1.8 angstroms resolution
Structure: Hen egg white lysozyme. Chain: a. Engineered: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Tissue: egg white
Resolution:
1.80Å     R-factor:   0.173    
Authors: I.Rayment,W.R.Rypniewski,H.M.Holden
Key ref:
W.R.Rypniewski et al. (1993). Structural consequences of reductive methylation of lysine residues in hen egg white lysozyme: an X-ray analysis at 1.8-A resolution. Biochemistry, 32, 9851-9858. PubMed id: 8373783 DOI: 10.1021/bi00088a041
Date:
02-Jun-93     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00698  (LYSC_CHICK) -  Lysozyme C
Seq:
Struc:
147 a.a.
129 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 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   3 terms 
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
DOI no: 10.1021/bi00088a041 Biochemistry 32:9851-9858 (1993)
PubMed id: 8373783  
 
 
Structural consequences of reductive methylation of lysine residues in hen egg white lysozyme: an X-ray analysis at 1.8-A resolution.
W.R.Rypniewski, H.M.Holden, I.Rayment.
 
  ABSTRACT  
 
Chemical modification of proteins has been and continues to be an important biochemical tool for the study of protein structure and function. One such type of approach has been the reductive methylation of lysine residues. In order to address the consequences of such methylation on the crystallization and structural properties of a protein, the three-dimensional structure of hen egg white lysozyme in which all lysine residues have been alkylated has been determined and refined to a nominal resolution of 1.8 A and a crystallographic R factor of 17.3%. Crystals used in the investigation were grown from 1.5-1.8 M MgSO4 and 50 mM Tris at pH 8.0 and belonged to the space group P2(1)2(1)2(1) with unit cell dimensions of a = 30.6 A, b = 56.3 A, c = 73.2 A, and one molecule per asymmetric unit. It was not possible to grow crystals of the modified lysozyme under the conditions normally employed for the hen egg white protein. Overall, the three-dimensional structures of the native lysozyme and the modified protein are very similar with only two surface loops differing to any significant extent. Specifically, the positions of the alpha-carbons for these two forms of the protein, excluding the surface loops, superimpose with a root-mean-square value of 0.40 A. The magnitude of the structural changes observed between the modified an unmodified forms of lysozyme is similar to that seen when an identical protein structure is solved in two different crystalline lattices.(ABSTRACT TRUNCATED AT 250 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21082721 G.J.Forse, N.Ram, D.R.Banatao, D.Cascio, M.R.Sawaya, H.E.Klock, S.A.Lesley, and T.O.Yeates (2011).
Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima.
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PDB code: 3o7o
21153892 K.W.Cheong, T.C.Leow, R.N.Rahman, M.Basri, M.B.Rahman, and A.B.Salleh (2011).
Reductive Alkylation Causes the Formation of a Molten Globule-Like Intermediate Structure in Geobacillus zalihae Strain T1 Thermostable Lipase.
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20824688 N.Cohen-Hadar, S.Lagziel-Simis, Y.Wine, F.Frolow, and A.Freeman (2011).
Re-structuring protein crystals porosity for biotemplating by chemical modification of lysine residues.
  Biotechnol Bioeng, 108, 1.  
20506323 P.Sledz, H.Zheng, K.Murzyn, M.Chruszcz, M.D.Zimmerman, M.D.Chordia, A.Joachimiak, and W.Minor (2010).
New surface contacts formed upon reductive lysine methylation: improving the probability of protein crystallization.
  Protein Sci, 19, 1395-1404.  
19390151 M.W.Vetting, S.S.Hegde, and J.S.Blanchard (2009).
Crystallization of a pentapeptide-repeat protein by reductive cyclic pentylation of free amines with glutaraldehyde.
  Acta Crystallogr D Biol Crystallogr, 65, 462-469.
PDB code: 2w7z
19551705 P.Pompach, P.Man, D.Kavan, K.Hofbauerová, V.Kumar, K.Bezouska, V.Havlícek, and P.Novák (2009).
Modified electrophoretic and digestion conditions allow a simplified mass spectrometric evaluation of disulfide bonds.
  J Mass Spectrom, 44, 1571-1578.  
19695097 R.M.Couñago, M.Davlieva, U.Strych, R.E.Hill, and K.L.Krause (2009).
Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames).
  BMC Struct Biol, 9, 53.
PDB code: 3ha1
19280122 S.J.Abraham, T.Kobayashi, R.J.Solaro, and V.Gaponenko (2009).
Differences in lysine pKa values may be used to improve NMR signal dispersion in reductively methylated proteins.
  J Biomol NMR, 43, 239-246.  
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.  
18310245 D.Takahashi, E.Nishimoto, T.Murase, and S.Yamashita (2008).
Protein-protein interaction on lysozyme crystallization revealed by rotational diffusion analysis.
  Biophys J, 94, 4484-4492.  
18677553 M.Sugahara, Y.Asada, K.Shimizu, H.Yamamoto, N.K.Lokanath, H.Mizutani, B.Bagautdinov, Y.Matsuura, M.Taketa, Y.Kageyama, N.Ono, Y.Morikawa, Y.Tanaka, H.Shimada, T.Nakamoto, M.Sugahara, M.Yamamoto, and N.Kunishima (2008).
High-throughput crystallization-to-structure pipeline at RIKEN SPring-8 Center.
  J Struct Funct Genomics, 9, 21-28.  
18819009 S.J.Abraham, S.Hoheisel, and V.Gaponenko (2008).
Detection of protein-ligand interactions by NMR using reductive methylation of lysine residues.
  J Biomol NMR, 42, 143-148.  
18825126 Y.Kim, P.Quartey, H.Li, L.Volkart, C.Hatzos, C.Chang, B.Nocek, M.Cuff, J.Osipiuk, K.Tan, Y.Fan, L.Bigelow, N.Maltseva, R.Wu, M.Borovilos, E.Duggan, M.Zhou, T.A.Binkowski, R.G.Zhang, and A.Joachimiak (2008).
Large-scale evaluation of protein reductive methylation for improving protein crystallization.
  Nat Methods, 5, 853-854.  
17617922 N.Shaw, C.Cheng, W.Tempel, J.Chang, J.Ng, X.Y.Wang, S.Perrett, J.Rose, Z.Rao, B.C.Wang, and Z.J.Liu (2007).
(NZ)CH...O contacts assist crystallization of a ParB-like nuclease.
  BMC Struct Biol, 7, 46.
PDB code: 1vk1
  17554174 W.Rauert, A.N.Eddine, S.H.Kaufmann, M.S.Weiss, and R.Janowski (2007).
Reductive methylation to improve crystallization of the putative oxidoreductase Rv0765c from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 507-511.  
  17142919 C.Rosenthal, U.Mueller, S.Panjikar, L.Sun, M.Ruppert, Y.Zhao, and J.Stöckigt (2006).
Expression, purification, crystallization and preliminary X-ray analysis of perakine reductase, a new member of the aldo-keto reductase enzyme superfamily from higher plants.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1286-1289.  
17050682 D.R.Banatao, D.Cascio, C.S.Crowley, M.R.Fleissner, H.L.Tienson, and T.O.Yeates (2006).
An approach to crystallizing proteins by synthetic symmetrization.
  Proc Natl Acad Sci U S A, 103, 16230-16235.
PDB codes: 2huk 2hul 2hum
  17142901 D.Shi, L.Caldovic, Z.Jin, X.Yu, Q.Qu, L.Roth, H.Morizono, Y.Hathout, N.M.Allewell, and M.Tuchman (2006).
Expression, crystallization and preliminary crystallographic studies of a novel bifunctional N-acetylglutamate synthase/kinase from Xanthomonas campestris homologous to vertebrate N-acetylglutamate synthase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1218-1222.  
16959567 G.Prehna, M.I.Ivanov, J.B.Bliska, and C.E.Stebbins (2006).
Yersinia virulence depends on mimicry of host Rho-family nucleotide dissociation inhibitors.
  Cell, 126, 869-880.
PDB codes: 2h7o 2h7v
16507363 M.Lilic, M.Vujanac, and C.E.Stebbins (2006).
A common structural motif in the binding of virulence factors to bacterial secretion chaperones.
  Mol Cell, 21, 653-664.
PDB codes: 2fm8 2fm9
17098187 T.S.Walter, C.Meier, R.Assenberg, K.F.Au, J.Ren, A.Verma, J.E.Nettleship, R.J.Owens, D.I.Stuart, and J.M.Grimes (2006).
Lysine methylation as a routine rescue strategy for protein crystallization.
  Structure, 14, 1617-1622.  
15681862 A.K.Shah, Z.J.Liu, P.D.Stewart, F.D.Schubot, J.P.Rose, M.G.Newton, and B.C.Wang (2005).
On increasing protein-crystallization throughput for X-ray diffraction studies.
  Acta Crystallogr D Biol Crystallogr, 61, 123-129.  
16211524 B.C.Wang, M.W.Adams, H.Dailey, L.DeLucas, M.Luo, J.Rose, R.Bunzel, T.Dailey, J.Habel, P.Horanyi, F.E.Jenney, I.Kataeva, H.S.Lee, S.Li, T.Li, D.Lin, Z.J.Liu, C.H.Luan, M.Mayer, L.Nagy, M.G.Newton, J.Ng, F.L.Poole, A.Shah, C.Shah, F.J.Sugar, and H.Xu (2005).
Protein production and crystallization at SECSG -- an overview.
  J Struct Funct Genomics, 6, 233-243.  
  16511062 F.J.López-Jaramillo, F.Pérez-Banderas, F.Hernández-Mateo, and F.Santoyo-González (2005).
Production, crystallization and X-ray characterization of chemically glycosylated hen egg-white lysozyme.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 435-438.  
15951425 R.J.Keenan, D.L.Siehl, R.Gorton, and L.A.Castle (2005).
DNA shuffling as a tool for protein crystallization.
  Proc Natl Acad Sci U S A, 102, 8887-8892.
PDB code: 2bsw
16211508 Z.J.Liu, A.K.Shah, J.E.Habel, J.D.Ng, I.Kataeva, H.Xu, P.Horanyi, H.Yang, J.Chang, M.Zhao, L.Huang, S.Chang, W.Tempel, L.Chen, W.Zhou, D.Lee, D.Lin, H.Zhang, M.G.Newton, J.Rose, and B.C.Wang (2005).
Salvaging Pyrococcus furiosus protein targets at SECSG.
  J Struct Funct Genomics, 6, 121-127.  
15502305 F.D.Schubot, and D.S.Waugh (2004).
A pivotal role for reductive methylation in the de novo crystallization of a ternary complex composed of Yersinia pestis virulence factors YopN, SycN and YscB.
  Acta Crystallogr D Biol Crystallogr, 60, 1981-1986.  
10089339 M.Kobayashi, M.Kubota, and Y.Matsuura (1999).
Crystallization and improvement of crystal quality for x-ray diffraction of maltooligosyl trehalose synthase by reductive methylation of lysine residues.
  Acta Crystallogr D Biol Crystallogr, 55, 931-933.  
8999862 T.N.Akopian, A.F.Kisselev, and A.L.Goldberg (1997).
Processive degradation of proteins and other catalytic properties of the proteasome from Thermoplasma acidophilum.
  J Biol Chem, 272, 1791-1798.  
8647813 S.Chacko, E.A.Padlan, S.Portolano, S.M.McLachlan, and B.Rapoport (1996).
Structural studies of human autoantibodies. Crystal structure of a thyroid peroxidase autoantibody Fab.
  J Biol Chem, 271, 12191-12198.
PDB code: 1vge
  7787065 A.J.Fisher, C.A.Smith, J.Thoden, R.Smith, K.Sutoh, H.M.Holden, and I.Rayment (1995).
Structural studies of myosin:nucleotide complexes: a revised model for the molecular basis of muscle contraction.
  Biophys J, 68, 19S.  
8519977 D.B.Stone, D.K.Schneider, Z.Huang, and R.A.Mendelson (1995).
The radius of gyration of native and reductively methylated myosin subfragment-1 from neutron scattering.
  Biophys J, 69, 767-776.  
8078940 D.B.Bivin, K.Ue, M.Khoroshev, and M.Morales (1994).
Effect of lysine methylation and other ATPase modulators on the active site of myosin subfragment 1.
  Proc Natl Acad Sci U S A, 91, 8665-8669.  
8203020 I.Rayment, and H.M.Holden (1994).
The three-dimensional structure of a molecular motor.
  Trends Biochem Sci, 19, 129-134.  
8167031 M.D.Rozycki, J.C.Myslik, C.E.Schutt, and U.Lindberg (1994).
Structural aspects of actin-binding proteins.
  Curr Opin Cell Biol, 6, 87-95.  
7832981 M.Zhang, E.Thulin, and H.J.Vogel (1994).
Reductive methylation and pKa determination of the lysine side chains in calbindin D9k.
  J Protein Chem, 13, 527-535.  
8069620 M.K.Reedy (1993).
Myosin-actin motors: the partnership goes atomic.
  Structure, 1, 1-5.  
8126212 R.G.Yount (1993).
Subfragment 1: the first crystalline motor.
  J Muscle Res Cell Motil, 14, 547-551.  
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.