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PDBsum entry 1dpp

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protein ligands Protein-protein interface(s) links
Peptide binding protein PDB id
1dpp
Jmol
Contents
Protein chains
507 a.a. *
Ligands
GLY-LEU ×4
* Residue conservation analysis
PDB id:
1dpp
Name: Peptide binding protein
Title: Dipeptide binding protein complex with glycyl-l-leucine
Structure: Dipeptide binding protein. Chain: a, c, e, g
Source: Escherichia coli. Organism_taxid: 562
Resolution:
3.20Å     R-factor:   0.223     R-free:   0.240
Authors: P.Dunten,S.L.Mowbray
Key ref:
P.Dunten and S.L.Mowbray (1995). Crystal structure of the dipeptide binding protein from Escherichia coli involved in active transport and chemotaxis. Protein Sci, 4, 2327-2334. PubMed id: 8563629 DOI: 10.1002/pro.5560041110
Date:
11-Aug-95     Release date:   07-Dec-95    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P23847  (DPPA_ECOLI) -  Periplasmic dipeptide transport protein
Seq:
Struc:
 
Seq:
Struc:
535 a.a.
507 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   3 terms 
  Biological process     transport   5 terms 
  Biochemical function     peptide binding     1 term  

 

 
DOI no: 10.1002/pro.5560041110 Protein Sci 4:2327-2334 (1995)
PubMed id: 8563629  
 
 
Crystal structure of the dipeptide binding protein from Escherichia coli involved in active transport and chemotaxis.
P.Dunten, S.L.Mowbray.
 
  ABSTRACT  
 
The Escherichia coli periplasmic dipeptide binding protein functions in both peptide transport and taxis toward peptides. The structure of the dipeptide binding protein in complex with Gly-Leu (glycyl-L-leucine) has been determined at 3.2 A resolution. The binding site for dipeptides is designed to recognize the ligand's backbone while providing space to accommodate a variety of side chains. Some repositioning of protein side chains lining the binding site must occur when the dipeptide's second residue is larger than leucine. The protein's fold is very similar to that of the Salmonella typhimurium oligopeptide binding protein, and a comparison of the structures reveals the structural basis for the dipeptide binding protein's preference for shorter peptides.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. BounddipeptideGly-Leuandres- iduesinvolvedinbindingitsbackboneare shown.The&strand(reidues 400-406) andthedipeptideareantiparallelwithre- spect tooneanother. Side chains of residues 20-21 and 403-406 havebeenomittedfor clarity.
Figure 6.
Fig. 6. a race f domain 11 fromtheoligopeptidebind- ing protein (A,pdbcodelola, with ligand Val-Lys-Pro-Gly) andthedipeptidebindingprotein (B). Boundpeptidesare shown as stick models, with theircarboxyterminus closest tothe viewer hen viewed in stereo.The viewis clippedat thebck or clarity.
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1995, 4, 2327-2334) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20233931 D.L.Englert, C.A.Adase, A.Jayaraman, and M.D.Manson (2010).
Repellent taxis in response to nickel ion requires neither Ni2+ transport nor the periplasmic NikA binding protein.
  J Bacteriol, 192, 2633-2637.  
20453143 W.X.Zhang, B.B.Xie, X.L.Chen, S.Dong, X.Y.Zhang, B.C.Zhou, and Y.Z.Zhang (2010).
Domains III and I-2{alpha}, at the entrance of the binding cleft, play an important role in cold adaptation of the periplasmic dipeptide-binding protein (DppA) from the deep-sea psychrophilic bacterium Pseudoalteromonas sp. strain SM9913.
  Appl Environ Microbiol, 76, 4354-4361.  
19019243 M.J.Cuneo, L.S.Beese, and H.W.Hellinga (2008).
Ligand-induced conformational changes in a thermophilic ribose-binding protein.
  BMC Struct Biol, 8, 50.
PDB codes: 2fn8 2fn9
18212011 M.K.Doeven, G.van den Bogaart, V.Krasnikov, and B.Poolman (2008).
Probing receptor-translocator interactions in the oligopeptide ABC transporter by fluorescence correlation spectroscopy.
  Biophys J, 94, 3956-3965.  
17242515 C.Addy, M.Ohara, F.Kawai, A.Kidera, M.Ikeguchi, S.Fuchigami, M.Osawa, I.Shimada, S.Y.Park, J.R.Tame, and J.G.Heddle (2007).
Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography.
  Acta Crystallogr D Biol Crystallogr, 63, 221-229.
PDB code: 2noo
16905647 S.Létoffé, P.Delepelaire, and C.Wandersman (2006).
The housekeeping dipeptide permease is the Escherichia coli heme transporter and functions with two optional peptide binding proteins.
  Proc Natl Acad Sci U S A, 103, 12891-12896.  
16045610 M.K.Doeven, J.Kok, and B.Poolman (2005).
Specificity and selectivity determinants of peptide transport in Lactococcus lactis and other microorganisms.
  Mol Microbiol, 57, 640-649.  
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.  
15502869 L.I.Leichert, and U.Jakob (2004).
Protein thiol modifications visualized in vivo.
  PLoS Biol, 2, e333.  
15610013 W.A.Williams, R.G.Zhang, M.Zhou, G.Joachimiak, P.Gornicki, D.Missiakas, and A.Joachimiak (2004).
The membrane-associated lipoprotein-9 GmpC from Staphylococcus aureus binds the dipeptide GlyMet via side chain interactions.
  Biochemistry, 43, 16193-16202.
PDB code: 1p99
14563878 J.Solomon, L.Su, S.Shyn, and A.D.Grossman (2003).
Isolation and characterization of mutants of the Bacillus subtilis oligopeptide permease with altered specificity of oligopeptide transport.
  J Bacteriol, 185, 6425-6433.  
14568145 Y.Sanz, F.Toldrá, P.Renault, and B.Poolman (2003).
Specificity of the second binding protein of the peptide ABC-transporter (Dpp) of Lactococcus lactis IL1403.
  FEMS Microbiol Lett, 227, 33-38.  
12381848 R.M.de Lorimier, J.J.Smith, M.A.Dwyer, L.L.Looger, K.M.Sali, C.D.Paavola, S.S.Rizk, S.Sadigov, D.W.Conrad, L.Loew, and H.W.Hellinga (2002).
Construction of a fluorescent biosensor family.
  Protein Sci, 11, 2655-2675.  
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.  
10762255 G.Fang, W.N.Konings, and B.Poolman (2000).
Kinetics and substrate specificity of membrane-reconstituted peptide transporter DtpT of Lactococcus lactis.
  J Bacteriol, 182, 2530-2535.  
10769143 Y.Sanz, F.C.Lanfermeijer, W.N.Konings, and B.Poolman (2000).
Kinetics and structural requirements for the binding protein of the Di-tripeptide transport system of Lactococcus lactis.
  Biochemistry, 39, 4855-4862.  
10545166 F.C.Lanfermeijer, A.Picon, W.N.Konings, and B.Poolman (1999).
Kinetics and consequences of binding of nona- and dodecapeptides to the oligopeptide binding protein (OppA) of Lactococcus lactis.
  Biochemistry, 38, 14440-14450.  
10066480 J.S.Lolkema, B.Poolman, and W.N.Konings (1998).
Bacterial solute uptake and efflux systems.
  Curr Opin Microbiol, 1, 248-253.  
9687374 M.S.Jurica, and B.L.Stoddard (1998).
Mind your B's and R's: bacterial chemotaxis, signal transduction and protein recognition.
  Structure, 6, 809-813.  
9245406 S.H.Sleigh, J.R.Tame, E.J.Dodson, and A.J.Wilkinson (1997).
Peptide binding in OppA, the crystal structures of the periplasmic oligopeptide binding protein in the unliganded form and in complex with lysyllysine.
  Biochemistry, 36, 9747-9758.
PDB codes: 1rkm 2rkm
8807882 A.J.Wilkinson (1996).
Accommodating structurally diverse peptides in proteins.
  Chem Biol, 3, 519-524.  
  8563630 P.Dunten, and S.L.Mowbray (1995).
Modeling of the structure of the Haemophilus influenzae heme-binding protein suggests a mode of heme interaction.
  Protein Sci, 4, 2335-2340.  
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.