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PDBsum entry 1b3f
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Peptide binding protein PDB id
1b3f

 

 

 

 

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Contents
Protein chain
517 a.a. *
Ligands
LYS-HIS-LYS
Metals
IUM ×8
Waters ×455
* Residue conservation analysis
PDB id:
1b3f
Name: Peptide binding protein
Title: Oligo-peptide binding protein (oppa) complexed with khk
Structure: Protein (oligo-peptide binding protein). Chain: a. Synonym: oppa. Engineered: yes. Protein (lys-his-lys). Chain: b. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 602. Gene: oppa. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.177     R-free:   0.217
Authors: J.R.H.Tame,A.J.Wilkinson
Key ref:
S.H.Sleigh et al. (1999). Crystallographic and calorimetric analysis of peptide binding to OppA protein. J Mol Biol, 291, 393-415. PubMed id: 10438628 DOI: 10.1006/jmbi.1999.2929
Date:
10-Dec-98     Release date:   16-Dec-98    
PROCHECK
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 Headers
 References

Protein chain
P06202  (OPPA_SALTY) -  Periplasmic oligopeptide-binding protein OppA from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Seq:
Struc: 		 
Seq:
Struc: 		543 a.a.
517 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1006/jmbi.1999.2929 J Mol Biol 291:393-415 (1999)
PubMed id: 10438628  
 
 
Crystallographic and calorimetric analysis of peptide binding to OppA protein.
S.H.Sleigh, P.R.Seavers, A.J.Wilkinson, J.E.Ladbury, J.R.Tame.
 
  ABSTRACT  
 
Isothermal titration calorimetry has been used to study the binding of 20 different peptides to the peptide binding protein OppA, and the crystal structures of the ligand complexes have been refined. This periplasmic binding protein, part of the oligopeptide permease system of Gram negative bacteria, has evolved to bind and enclose small peptides of widely varying sequences. The peptides used in this study have the sequence Lys-X-Lys, where X is any of the 20 commonly occurring amino acids. The various side-chains found at position 2 on the ligand fit into a hydrated pocket. The majority of side-chains are restrained to particular conformations within the pocket. Water molecules act as flexible adapters, matching the hydrogen-bonding requirements of the protein and ligand and shielding charges on the buried ligand. This use of water by OppA to broaden the repertoire of its binding site is not unique, but contrasts sharply with other proteins which use water to help bind ligands highly selectively. Predicting the thermodynamics of binding from the structure of the complexes is highly complicated by the influence of water on the system.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Bar chart showing the logarithm of KD (nM) for each of the ligands, in ascending order.
 
  The above figure is reprinted by permission from Elsevier: J Mol Biol (1999, 291, 393-415) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20582607 F.Tian, L.Yang, F.Lv, X.Luo, and Y.Pan (2011).
Why OppA protein can bind sequence-independent peptides? A combination of QM/MM, PB/SA, and structure-based QSAR analyses.
  Amino Acids, 40, 493-503.  
  21469159 S.Y.Lu, Y.J.Jiang, J.Lv, J.W.Zou, and T.X.Wu (2011).
Role of bridging water molecules in GSK3β-inhibitor complexes: insights from QM/MM, MD, and molecular docking studies.
  J Comput Chem, 32, 1907-1918.  
19549999 E.B.Unal, A.Gursoy, and B.Erman (2009).
Conformational energies and entropies of peptides, and the peptide-protein binding problem.
  Phys Biol, 6, 36014.  
19801540 M.J.Cuneo, L.S.Beese, and H.W.Hellinga (2009).
Structural analysis of semi-specific oligosaccharide recognition by a cellulose-binding protein of thermotoga maritima reveals adaptations for functional diversification of the oligopeptide periplasmic binding protein fold.
  J Biol Chem, 284, 33217-33223.
PDB codes: 2o7i 3i5o
17855399 H.Cheng, B.H.Kim, and N.V.Grishin (2008).
MALISAM: a database of structurally analogous motifs in proteins.
  Nucleic Acids Res, 36, D211-D217.  
18086667 S.Chopra, R.M.Dooling, C.G.Horner, and E.E.Howell (2008).
A balancing act between net uptake of water during dihydrofolate binding and net release of water upon NADPH binding in R67 dihydrofolate reductase.
  J Biol Chem, 283, 4690-4698.  
17638325 A.Marchand, D.Marchand, R.Busson, P.Marlière, and P.Herdewijn (2007).
Synthesis of a pyridoxine-peptide based delivery system for nucleotides.
  Chem Biodivers, 4, 1450-1465.  
17873047 H.Zhang, J.P.Herman, H.Bolton, Z.Zhang, S.Clark, and L.Xun (2007).
Evidence that bacterial ABC-type transporter imports free EDTA for metabolism.
  J Bacteriol, 189, 7991-7997.  
16689642 Y.Levy, and J.N.Onuchic (2006).
Water mediation in protein folding and molecular recognition.
  Annu Rev Biophys Biomol Struct, 35, 389-415.  
16212506 A.R.Osborne, T.A.Rapoport, and B.van den Berg (2005).
Protein translocation by the Sec61/SecY channel.
  Annu Rev Cell Dev Biol, 21, 529-550.  
15608125 S.D.Sharrow, K.A.Edmonds, M.A.Goodman, M.V.Novotny, and M.J.Stone (2005).
Thermodynamic consequences of disrupting a water-mediated hydrogen bond network in a protein:pheromone complex.
  Protein Sci, 14, 249-256.  
15256599 A.R.Osborne, W.M.Clemons, and T.A.Rapoport (2004).
A large conformational change of the translocation ATPase SecA.
  Proc Natl Acad Sci U S A, 101, 10937-10942.
PDB codes: 1tf2 1tf5
15281134 D.B.Sherman, S.Zhang, J.B.Pitner, and A.Tropsha (2004).
Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method.
  Proteins, 56, 828-838.  
14679224 X.G.Wang, J.M.Kidder, J.P.Scagliotti, M.S.Klempner, R.Noring, and L.T.Hu (2004).
Analysis of differences in the functional properties of the substrate binding proteins of the Borrelia burgdorferi oligopeptide permease (Opp) operon.
  J Bacteriol, 186, 51-60.  
14993602 Y.Levy, and J.N.Onuchic (2004).
Water and proteins: a love-hate relationship.
  Proc Natl Acad Sci U S A, 101, 3325-3326.  
12538891 A.M.Hays, H.B.Gray, and D.B.Goodin (2003).
Trapping of peptide-based surrogates in an artificially created channel of cytochrome c peroxidase.
  Protein Sci, 12, 278-287.  
12444085 A.Yokota, K.Tsumoto, M.Shiroishi, H.Kondo, and I.Kumagai (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.
PDB codes: 1j1o 1j1p 1j1x
12447911 E.Yuriev, and P.A.Ramsland (2002).
Mcg light chain dimer as a model system for ligand design: a docking study.
  J Mol Recognit, 15, 331-340.  
11371463 D.Jain, K.J.Kaur, and D.M.Salunke (2001).
Plasticity in protein-peptide recognition: crystal structures of two different peptides bound to concanavalin A.
  Biophys J, 80, 2912-2921.
PDB codes: 1jui 1jyc
11391788 E.Yuriev, P.A.Ramsland, and A.B.Edmundson (2001).
Docking of combinatorial peptide libraries into a broadly cross-reactive human IgM.
  J Mol Recognit, 14, 172-184.  
11514673 K.M.Peterson, K.V.Gopalan, A.Nandy, and D.K.Srivastava (2001).
Influence of Glu-376 --> Gln mutation on enthalpy and heat capacity changes for the binding of slightly altered ligands to medium chain acyl-CoA dehydrogenase.
  Protein Sci, 10, 1822-1834.  
11504727 M.Goel, D.Jain, K.J.Kaur, R.Kenoth, B.G.Maiya, M.J.Swamy, and D.M.Salunke (2001).
Functional equality in the absence of structural similarity: an added dimension to molecular mimicry.
  J Biol Chem, 276, 39277-39281.
PDB code: 1jn2
11354461 N.J.Marshall, B.M.Grail, and J.W.Payne (2001).
Predominant torsional forms adopted by oligopeptide conformers in solution: parameters for molecular recognition.
  J Pept Sci, 7, 175-189.  
11320310 T.J.Oldfield (2001).
X-LIGAND: an application for the automated addition of flexible ligands into electron density.
  Acta Crystallogr D Biol Crystallogr, 57, 696-705.  
10899119 F.C.Lanfermeijer, F.J.Detmers, W.N.Konings, and B.Poolman (2000).
On the binding mechanism of the peptide receptor of the oligopeptide transport system of Lactococcus lactis.
  EMBO J, 19, 3649-3656.  
11050157 F.J.Detmers, F.C.Lanfermeijer, R.Abele, R.W.Jack, R.Tampe, W.N.Konings, and B.Poolman (2000).
Combinatorial peptide libraries reveal the ligand-binding mechanism of the oligopeptide receptor OppA of Lactococcus lactis.
  Proc Natl Acad Sci U S A, 97, 12487-12492.  
11087406 J.R.Barbier, S.MacLean, P.Morley, J.F.Whitfield, and G.E.Willick (2000).
Structure and activities of constrained analogues of human parathyroid hormone and parathyroid hormone-related peptide: implications for receptor-activating conformations of the hormones.
  Biochemistry, 39, 14522-14530.  
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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