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PDBsum entry 1j1x
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protein Protein-protein interface(s) links
Immune system/hydrolase PDB id
1j1x

 

 

 

 

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Contents
Protein chains
107 a.a. *
114 a.a. *
129 a.a. *
Waters ×357
* Residue conservation analysis
PDB id:
1j1x
Name: Immune system/hydrolase
Title: Crystal structure of hyhel-10 fv mutant ls93a complexed with hen egg white lysozyme
Structure: Lysozyme binding ig kappa chain v23-j2 region. Chain: l. Synonym: lysozyme antibody, hyhel-10. Engineered: yes. Mutation: yes. Ig vh,anti-lysozyme. Chain: h. Synonym: lysozyme antibody, hyhel-10. Engineered: yes.
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gallus gallus. Chicken. Organism_taxid: 9031. Tissue: egg white
Biol. unit: Trimer (from PQS)
Resolution:
1.80Å     R-factor:   0.189     R-free:   0.217
Authors: A.Yokota,K.Tsumoto,M.Shiroishi,H.Kondo,I.Kumagai
Key ref:
A.Yokota et al. (2003). The role of hydrogen bonding via interfacial water molecules in antigen-antibody complexation. The HyHEL-10-HEL interaction. J Biol Chem, 278, 5410-5418. PubMed id: 12444085 DOI: 10.1074/jbc.M210182200
Date:
20-Dec-02     Release date:   14-Jan-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01642  (KV5A9_MOUSE) -  Immunoglobulin kappa variable 5-48 (Fragment) from Mus musculus
Seq:
Struc: 		115 a.a.
107 a.a.*
Protein chain
Pfam   ArchSchema ?
P01823  (HVM47_MOUSE) -  Ig heavy chain V region 36-60 from Mus musculus
Seq:
Struc: 		113 a.a.
114 a.a.*
Protein chain
Pfam   ArchSchema ?
P00698  (LYSC_CHICK) -  Lysozyme C from Gallus gallus
Seq:
Struc: 		147 a.a.
129 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 33 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chain Y: 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.

 

 
DOI no: 10.1074/jbc.M210182200 J Biol Chem 278:5410-5418 (2003)
PubMed id: 12444085  
 
 
The role of hydrogen bonding via interfacial water molecules in antigen-antibody complexation. The HyHEL-10-HEL interaction.
A.Yokota, K.Tsumoto, M.Shiroishi, H.Kondo, I.Kumagai.
 
  ABSTRACT  
 
To study the role of hydrogen bonding via interfacial water molecules in protein-protein interactions, we examined the interaction between hen egg white lysozyme (HEL) and its HyHEL-10 variable domain fragment (Fv) antibody. We constructed three antibody mutants (l-Y50F, l-S91A, and l-S93A) and investigated the interactions between the mutant Fvs and HEL. Isothermal titration calorimetry indicated that the mutations significantly decreased the negative enthalpy change (8-25 kJ mol(-1)), despite some offset by a favorable entropy change. X-ray crystallography demonstrated that the complexes had nearly identical structures, including the positions of the interfacial water molecules. Taken together, the isothermal titration calorimetric and x-ray crystallographic results indicate that hydrogen bonding via interfacial water enthalpically contributes to the Fv-HEL interaction despite the partial offset because of entropy loss, suggesting that hydrogen bonding stiffens the antigen-antibody complex.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Hydrogen bonding via interfacial water molecules at the HyHEL-10 Fv-HEL interface. C stick diagram of the wild-type Fv-HEL complex. VL, green; VH, sky blue; HEL, pink. The residues investigated in this report are drawn in blue. A, overall structure. B, local structures around the target sites. Generated with WebLab Viewer (Molecular Simulations Inc., San Diego, CA). The antibody residues are numbered according to Kabat et al. (75). 		Figure 6.
Fig. 6. Comparison of local structures in the LY50F-HEL and WT-HEL complexes. Region around the mutated site (50 of VL). Hydrogen bonds made by water molecules are depicted as dotted lines. The positions marked W correspond to the water molecules (parentheses indicate wild-type water molecules). L-Y50F antibody VL chain, sky blue; VH chain, green; HEL, pink; water, red; WT-HEL complex, gray.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 5410-5418) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21161086 M.Ui, Y.Tanaka, T.Tsumuraya, I.Fujii, M.Inoue, M.Hirama, and K.Tsumoto (2011).
Structural and energetic hot-spots for the interaction between a ladder-like polycyclic ether and the anti-ciguatoxin antibody 10C9Fab.
  Mol Biosyst, 7, 793-798.  
20038580 A.Yokota, K.Tsumoto, M.Shiroishi, T.Nakanishi, H.Kondo, and I.Kumagai (2010).
Contribution of asparagine residues to the stabilization of a proteinaceous antigen-antibody complex, HyHEL-10-hen egg white lysozyme.
  J Biol Chem, 285, 7686-7696.
PDB codes: 3a67 3a6b 3a6c
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.  
18704951 S.Szep, S.Park, E.T.Boder, G.D.Van Duyne, and J.G.Saven (2009).
Structural coupling between FKBP12 and buried water.
  Proteins, 74, 603-611.
PDB codes: 2ppn 2ppo 2ppp
18227432 T.Nakanishi, K.Tsumoto, A.Yokota, H.Kondo, and I.Kumagai (2008).
Critical contribution of VH-VL interaction to reshaping of an antibody: the case of humanization of anti-lysozyme antibody, HyHEL-10.
  Protein Sci, 17, 261-270.
PDB codes: 2eiz 2eks 2yss
18604448 Y.Liang (2008).
Applications of isothermal titration calorimetry in protein science.
  Acta Biochim Biophys Sin (Shanghai), 40, 565-576.  
17471455 H.H.Bui, A.J.Schiewe, and I.S.Haworth (2007).
WATGEN: an algorithm for modeling water networks at protein-protein interfaces.
  J Comput Chem, 28, 2241-2251.  
17242738 Z.Li, and T.Lazaridis (2007).
Water at biomolecular binding interfaces.
  Phys Chem Chem Phys, 9, 573-581.  
16165056 J.A.Gomes, J.L.Gossage, H.Balu, M.Kesmez, F.Bowen, R.S.Lumpkin, and D.L.Cocke (2005).
Experimental and theoretical study of the atmospherically important O2-H2O complex.
  Spectrochim Acta A Mol Biomol Spectrosc, 61, 3082-3086.  
15384176 M.J.Cliff, A.Gutierrez, and J.E.Ladbury (2004).
A survey of the year 2003 literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 17, 513-523.  
15103623 S.Vega, L.W.Kang, A.Velazquez-Campoy, Y.Kiso, L.M.Amzel, and E.Freire (2004).
A structural and thermodynamic escape mechanism from a drug resistant mutation of the HIV-1 protease.
  Proteins, 55, 594-602.
PDB codes: 1mrw 1mrx 1msm 1msn
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.

 

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