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PDBsum entry 2ihl

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Hydrolase(o-glycosyl) PDB id
2ihl
Jmol
Contents
Protein chain
129 a.a. *
Metals
_NA
Waters ×151
* Residue conservation analysis
PDB id:
2ihl
Name: Hydrolase(o-glycosyl)
Title: Lysozyme (E.C.3.2.1.17) (japanese quail)
Structure: Japanese quail egg white lysozyme. Chain: a. Engineered: yes
Source: Coturnix japonica. Japanese quail. Organism_taxid: 93934
Biol. unit: Dimer (from PQS)
Resolution:
1.40Å     R-factor:   0.165    
Authors: A.Houdusse,G.A.Bentley,R.J.Poljak,H.Souchon,Z.Zhang
Key ref: V.Chitarra et al. (1993). Three-dimensional structure of a heteroclitic antigen-antibody cross-reaction complex. Proc Natl Acad Sci U S A, 90, 7711-7715. PubMed id: 8356074 DOI: 10.1073/pnas.90.16.7711
Date:
29-Jun-93     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00701  (LYSC_COTJA) -  Lysozyme C
Seq:
Struc:
147 a.a.
129 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   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
DOI no: 10.1073/pnas.90.16.7711 Proc Natl Acad Sci U S A 90:7711-7715 (1993)
PubMed id: 8356074  
 
 
Three-dimensional structure of a heteroclitic antigen-antibody cross-reaction complex.
V.Chitarra, P.M.Alzari, G.A.Bentley, T.N.Bhat, J.L.Eiselé, A.Houdusse, J.Lescar, H.Souchon, R.J.Poljak.
 
  ABSTRACT  
 
Although antibodies are highly specific, cross-reactions are frequently observed. To understand the molecular basis of this phenomenon, we studied the anti-hen egg lysozyme (HEL) monoclonal antibody (mAb) D11.15, which cross-reacts with several avian lysozymes, in some cases with a higher affinity (heteroclitic binding) than for HEL. We have determined the crystal structure of the Fv fragment of D11.15 complexed with pheasant egg lysozyme (PHL). In addition, we have determined the structure of PHL, Guinea fowl egg lysozyme, and Japanese quail egg lysozyme. Differences in the affinity of D11.15 for the lysozymes appear to result from sequence substitutions in these antigens at the interface with the antibody. More generally, cross-reactivity is seen to require a stereochemically permissive environment for the variant antigen residues at the antibody-antigen interface.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21213247 P.L.Kastritis, I.H.Moal, H.Hwang, Z.Weng, P.A.Bates, A.M.Bonvin, and J.Janin (2011).
A structure-based benchmark for protein-protein binding affinity.
  Protein Sci, 20, 482-491.  
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.  
19264660 R.Rajamanonmani, C.Nkenfou, P.Clancy, Y.H.Yau, S.G.Shochat, S.Sukupolvi-Petty, W.Schul, M.S.Diamond, S.G.Vasudevan, and J.Lescar (2009).
On a mouse monoclonal antibody that neutralizes all four dengue virus serotypes.
  J Gen Virol, 90, 799-809.  
19166328 S.Mohan, K.Kourentzi, K.A.Schick, C.Uehara, C.A.Lipschultz, M.Acchione, M.E.Desantis, S.J.Smith-Gill, and R.C.Willson (2009).
Association energetics of cross-reactive and specific antibodies.
  Biochemistry, 48, 1390-1398.  
18068724 C.H.Bell, R.Pantophlet, A.Schiefner, L.A.Cavacini, R.L.Stanfield, D.R.Burton, and I.A.Wilson (2008).
Structure of antibody F425-B4e8 in complex with a V3 peptide reveals a new binding mode for HIV-1 neutralization.
  J Mol Biol, 375, 969-978.
PDB code: 2qsc
17942558 D.Luo, T.Xu, C.Hunke, G.Grüber, S.G.Vasudevan, and J.Lescar (2008).
Crystal structure of the NS3 protease-helicase from dengue virus.
  J Virol, 82, 173-183.
PDB code: 2vbc
18234071 V.Moreau, C.Fleury, D.Piquer, C.Nguyen, N.Novali, S.Villard, D.Laune, C.Granier, and F.Molina (2008).
PEPOP: computational design of immunogenic peptides.
  BMC Bioinformatics, 9, 71.  
17173281 F.Autore, S.Melchiorre, J.Kleinjung, W.D.Morgan, and F.Fraternali (2007).
Interaction of malaria parasite-inhibitory antibodies with the merozoite surface protein MSP1(19) by computational docking.
  Proteins, 66, 513-527.  
16537393 E.De Genst, K.Silence, K.Decanniere, K.Conrath, R.Loris, J.Kinne, S.Muyldermans, and L.Wyns (2006).
Molecular basis for the preferential cleft recognition by dromedary heavy-chain antibodies.
  Proc Natl Acad Sci U S A, 103, 4586-4591.
PDB codes: 1zv5 1zvh 1zvy
16489928 H.Younus, S.Jamal, B.Ahmad, and M.Saleemuddin (2006).
Investigation of conformational changes induced by binding of pancreatic RNase to anti-RNase IgG derived Fab monomer using optical procedures.
  Biochemistry (Mosc), 71, 218-221.  
16487065 P.Gupta, M.Saleemuddin, and R.H.Khan (2006).
Hydrophobic interactions are the prevalent force in bromelain:Fab' complex.
  Biochemistry (Mosc), 71, S31-S37.  
16053383 J.Sanders, F.Allen, J.Jeffreys, J.Bolton, T.Richards, H.Depraetere, N.Nakatake, M.Evans, A.Kiddie, L.D.Premawardhana, D.Y.Chirgadze, R.N.Miguel, T.L.Blundell, J.Furmaniak, and B.R.Smith (2005).
Characteristics of a monoclonal antibody to the thyrotropin receptor that acts as a powerful thyroid-stimulating autoantibody antagonist.
  Thyroid, 15, 672-682.  
14988501 A.Cauerhff, F.A.Goldbaum, and B.C.Braden (2004).
Structural mechanism for affinity maturation of an anti-lysozyme antibody.
  Proc Natl Acad Sci U S A, 101, 3539-3544.
PDB code: 1p2c
15162489 S.Liu, C.Zhang, H.Zhou, and Y.Zhou (2004).
A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.
  Proteins, 56, 93.  
14581222 S.Mohan, N.Sinha, and S.J.Smith-Gill (2003).
Modeling the binding sites of anti-hen egg white lysozyme antibodies HyHEL-8 and HyHEL-26: an insight into the molecular basis of antibody cross-reactivity and specificity.
  Biophys J, 85, 3221-3236.  
12237453 J.Pons, J.R.Stratton, and J.F.Kirsch (2002).
How do two unrelated antibodies, HyHEL-10 and F9.13.7, recognize the same epitope of hen egg-white lysozyme?
  Protein Sci, 11, 2308-2315.  
10899782 D.Fleury, R.S.Daniels, J.J.Skehel, M.Knossow, and T.Bizebard (2000).
Structural evidence for recognition of a single epitope by two distinct antibodies.
  Proteins, 40, 572-578.
PDB code: 1eo8
10737939 D.W.Ritchie, and G.J.Kemp (2000).
Protein docking using spherical polar Fourier correlations.
  Proteins, 39, 178-194.  
10828942 Y.Li, H.Li, S.J.Smith-Gill, and R.A.Mariuzza (2000).
Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63(,).
  Biochemistry, 39, 6296-6309.
PDB codes: 1dqj 1dqm 1dqq
10354424 C.A.Sotriffer, W.Flader, A.Cooper, B.M.Rode, D.S.Linthicum, K.R.Liedl, and J.M.Varga (1999).
Ligand binding by antibody IgE Lb4: assessment of binding site preferences using microcalorimetry, docking, and free energy simulations.
  Biophys J, 76, 2966-2977.  
10664845 M.Shimoda, Y.Inoue, N.Azuma, and C.Kanno (1999).
Local antibody response in Peyer's patches to the orally administered dietary protein antigen.
  Biosci Biotechnol Biochem, 63, 2123-2129.  
10024024 N.Kessler, D.Perl-Treves, L.Addadi, and M.Eisenstein (1999).
Structural and chemical complementarity between antibodies and the crystal surfaces they recognize.
  Proteins, 34, 383-394.  
9692956 P.S.Pruett, and G.M.Air (1998).
Critical interactions in binding antibody NC41 to influenza N9 neuraminidase: amino acid contacts on the antibody heavy chain.
  Biochemistry, 37, 10660-10670.  
9413989 A.Kramer, T.Keitel, K.Winkler, W.Stöcklein, W.Höhne, and J.Schneider-Mergener (1997).
Molecular basis for the binding promiscuity of an anti-p24 (HIV-1) monoclonal antibody.
  Cell, 91, 799-809.  
9145111 G.Otting, E.Liepinsh, B.Halle, and U.Frey (1997).
NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules.
  Nat Struct Biol, 4, 396-404.  
9434905 I.A.Wilson, and K.C.Garcia (1997).
T-cell receptor structure and TCR complexes.
  Curr Opin Struct Biol, 7, 839-848.  
9413990 T.Keitel, A.Kramer, H.Wessner, C.Scholz, J.Schneider-Mergener, and W.Höhne (1997).
Crystallographic analysis of anti-p24 (HIV-1) monoclonal antibody cross-reactivity and polyspecificity.
  Cell, 91, 811-820.
PDB codes: 1bog 1cfn 1cfq 1cfs 1cft 1hi6
8784355 A.Desmyter, T.R.Transue, M.A.Ghahroudi, M.H.Thi, F.Poortmans, R.Hamers, S.Muyldermans, and L.Wyns (1996).
Crystal structure of a camel single-domain VH antibody fragment in complex with lysozyme.
  Nat Struct Biol, 3, 803-811.
PDB code: 1mel
8952503 B.A.Fields, F.A.Goldbaum, W.Dall'Acqua, E.L.Malchiodi, A.Cauerhff, F.P.Schwarz, X.Ysern, R.J.Poljak, and R.A.Mariuzza (1996).
Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three Fv mutants complexed with lysozyme.
  Biochemistry, 35, 15494-15503.
PDB codes: 1kip 1kiq 1kir
8552677 D.R.Davies, and G.H.Cohen (1996).
Interactions of protein antigens with antibodies.
  Proc Natl Acad Sci U S A, 93, 7.  
7705353 F.P.Schwarz, D.Tello, F.A.Goldbaum, R.A.Mariuzza, and R.J.Poljak (1995).
Thermodynamics of antigen-antibody binding using specific anti-lysozyme antibodies.
  Eur J Biochem, 228, 388-394.  
7716167 J.Janin (1995).
Elusive affinities.
  Proteins, 21, 30-39.  
  7795528 M.A.Turner, and P.L.Howell (1995).
Structures of partridge egg-white lysozyme with and without tri-N-acetylchitotriose inhibitor at 1.9 A resolution.
  Protein Sci, 4, 442-449.  
7986568 D.Tello, E.Eisenstein, F.P.Schwarz, F.A.Goldbaum, B.A.Fields, R.A.Mariuzza, and R.J.Poljak (1994).
Structural and physicochemical analysis of the reaction between the anti-lysozyme antibody D1.3 and the anti-idiotopic antibodies E225 and E5.2.
  J Mol Recognit, 7, 57-62.  
7511810 J.Cherfils, T.Bizebard, M.Knossow, and J.Janin (1994).
Rigid-body docking with mutant constraints of influenza hemagglutinin with antibody HC19.
  Proteins, 18, 8.  
  8061608 J.Lescar, H.Souchon, and P.M.Alzari (1994).
Crystal structures of pheasant and guinea fowl egg-white lysozymes.
  Protein Sci, 3, 788-798.
PDB codes: 1ghl 1hhl
7704531 O.Perisic, P.A.Webb, P.Holliger, G.Winter, and R.L.Williams (1994).
Crystal structure of a diabody, a bivalent antibody fragment.
  Structure, 2, 1217-1226.
PDB code: 1lmk
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.