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PDBsum entry 2jel
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protein ligands Protein-protein interface(s) links
Complex (antibody/antigen) PDB id
2jel

 

 

 

 

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Contents
Protein chains
217 a.a. *
218 a.a. *
85 a.a. *
Ligands
SO4 ×2
Waters ×67
* Residue conservation analysis
PDB id:
2jel
Name: Complex (antibody/antigen)
Title: Jel42 fab/hpr complex
Structure: Jel42 fab fragment. Chain: l. Jel42 fab fragment. Chain: h. Histidine-containing protein. Chain: p. Synonym: hpr
Source: Mus musculus. House mouse. Organism_taxid: 10090. Strain: balb/c. Escherichia coli. Organism_taxid: 562
Biol. unit: Trimer (from PQS)
Resolution:
2.50Å     R-factor:   0.210     R-free:   0.280
Authors: L.Prasad,E.B.Waygood,J.S.Lee,L.T.J.Delbaere
Key ref:
L.Prasad et al. (1998). The 2.5 A resolution structure of the jel42 Fab fragment/HPr complex. J Mol Biol, 280, 829-845. PubMed id: 9671553 DOI: 10.1006/jmbi.1998.1888
Date:
24-Feb-98     Release date:   27-May-98    
Supersedes: 1jel
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 217 a.a.
Protein chain
No UniProt id for this chain
Struc: 218 a.a.
Protein chain
Pfam   ArchSchema ?
P0AA04  (PTHP_ECOLI) -  Phosphocarrier protein HPr from Escherichia coli (strain K12)
Seq:
Struc: 		85 a.a.
85 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1006/jmbi.1998.1888 J Mol Biol 280:829-845 (1998)
PubMed id: 9671553  
 
 
The 2.5 A resolution structure of the jel42 Fab fragment/HPr complex.
L.Prasad, E.B.Waygood, J.S.Lee, L.T.Delbaere.
 
  ABSTRACT  
 
The tertiary structure of Jel42 Fab fragment complexed with HPr, a phosphocarrier protein of the phosphoenolpyruvate:sugar phosphotransferase system of Escherichia coli, has been determined at 2.5 A resolution. X-ray diffraction from a larger crystal provided 22,067 unique reflections as compared to 14,763 unique reflections (2.8 A resolution), which were obtained previously from a smaller crystal. The higher resolution allowed for more precise location of amino acid side-chains and for the location of well-ordered water molecules. Five more residues in the Fab fragment are found to be involved in binding HPr and two additional residues are identified as part of the epitope, bringing the totals to 24 and 16, respectively. At least nine water molecules are found at the interface between the two proteins, and these mediate hydrogen bonding interactions between the Fab fragment and HPr. Three additional hydrogen bonds have been identified (bringing the total to ten) and one salt-bridge occurs between LysL50 of the L2 complementarity-determining region (CDR) and GluP66 of HPr. This salt-bridge is the only interaction between HPr and CDRL2; thus all six CDRs are involved in binding. Inspection and empirical energy minimization of mutant HPrs in the complex indicate that, in some cases in the binding interaction, water molecules may compensate for residue alterations. Binding to the mutant SerP64Tyr HPr may require a movement of the HPr main chain. The active centre region of HPr, which is not involved in binding the antibody, and which was not resolved in the 2.8 A resolution structure of the complex, was determined. This active centre determined at pH 5.8, which is completely free of intermolecular contacts due to crystal packing, shows a potential hydrogen bond between the AsnP12 OD1 atom and the HisP15 NE2 atom, and no involvement of the C terminus with HisP15. The HisP15 ND1 atom is the site of phosphorylation in HPr. Although a specific amino acid at residue 12 is not conserved in HPr molecules from all species, a hydrogen bond between the side-chains of residue 12 and HisP15 may be a conserved feature of the active centres.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Contacts between the Jel42 Fab fragment and HPr mediated through water molecules. The Figure was made using the program SETOR (Evans, 1993). Side-chain colours are as in Figure 3. 		Figure 9.
Figure 9. Superposition of the C a atom trace of wild- type HPr (pink), S46D mutant of HPr (blue) and HPr complexed to the Jel42 Fab fragment (gold). The Figure was made using the program SETOR (Evans, 1993).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 280, 829-845) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20441761 G.Scarabelli, G.Morra, and G.Colombo (2010).
Predicting interaction sites from the energetics of isolated proteins: a new approach to epitope mapping.
  Biophys J, 98, 1966-1975.  
19361425 C.E.Leysath, A.F.Monzingo, J.A.Maynard, J.Barnett, G.Georgiou, B.L.Iverson, and J.D.Robertus (2009).
Crystal structure of the engineered neutralizing antibody M18 complexed to domain 4 of the anthrax protective antigen.
  J Mol Biol, 387, 680-693.
PDB codes: 3esu 3esv 3et9 3etb
19564948 X.Du, J.Cheng, and J.Song (2009).
Identifying protein-protein interaction sites using covering algorithm.
  Int J Mol Sci, 10, 2190-2202.  
18702519 S.Napper, L.Prasad, and L.T.Delbaere (2008).
Structural investigation of a phosphorylation-catalyzed, isoaspartate-free, protein succinimide: crystallographic structure of post-succinimide His15Asp histidine-containing protein.
  Biochemistry, 47, 9486-9496.
PDB code: 3ccd
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.  
15778956 D.Segal, and M.Eisenstein (2005).
The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking.
  Proteins, 59, 580-591.  
15162493 A.Berchanski, B.Shapira, and M.Eisenstein (2004).
Hydrophobic complementarity in protein-protein docking.
  Proteins, 56, 130-142.  
12784363 E.Ben-Zeev, and M.Eisenstein (2003).
Weighted geometric docking: incorporating external information in the rotation-translation scan.
  Proteins, 52, 24-27.  
11847280 A.Heifetz, E.Katchalski-Katzir, and M.Eisenstein (2002).
Electrostatics in protein-protein docking.
  Protein Sci, 11, 571-587.  
10668628 S.J.Brokx, S.Napper, G.Wong, A.Mirza, F.Georges, L.T.Delbaere, and E.B.Waygood (1999).
Identification of the Escherichia coli enzyme I binding site in histidine-containing protein, HPr, by the effects of mutagenesis.
  Biochem Cell Biol, 77, 507-513.  
10419492 S.Napper, L.T.Delbaere, and E.B.Waygood (1999).
The aspartyl replacement of the active site histidine in histidine-containing protein, HPr, of the Escherichia coli Phosphoenolpyruvate:Sugar phosphotransferase system can accept and donate a phosphoryl group. Spontaneous dephosphorylation of acyl-phosphate autocatalyzes an internal cyclization.
  J Biol Chem, 274, 21776-21782.
PDB codes: 1cm2 1cm3
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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