 |
PDBsum entry 1dpp
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Peptide binding protein
|
PDB id
|
|
|
|
1dpp
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Protein Sci
4:2327-2334
(1995)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
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
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
L.I.Leichert,
and
U.Jakob
(2004).
Protein thiol modifications visualized in vivo.
|
| |
PLoS Biol,
2,
e333.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
J.S.Lolkema,
B.Poolman,
and
W.N.Konings
(1998).
Bacterial solute uptake and efflux systems.
|
| |
Curr Opin Microbiol,
1,
248-253.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
A.J.Wilkinson
(1996).
Accommodating structurally diverse peptides in proteins.
|
| |
Chem Biol,
3,
519-524.
|
|
|
|
|
|
|
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.
|
|
Links
