PDBsum entry 1jev

Complex (peptide transport/peptide)

PDB id

1jev

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Contents

			Protein chain

					517 a.a. *

			Ligands

					LYS-TRP-LYS

			Metals

					IUM ×8

			Waters ×522

* Residue conservation analysis

PDB id:

1jev

Links

Name:

Complex (peptide transport/peptide)

Title:

Oligo-peptide binding protein (oppa) complexed with kwk

Structure:

Oligo-peptide binding protein. Chain: a. Synonym: oppa. Peptide lys trp lys. Chain: b. Engineered: yes

Source:

Salmonella typhimurium. Organism_taxid: 602.

Biol. unit:

Dimer (from PQS)

Resolution:

1.30Å

R-factor:

0.203

R-free:

0.226

Authors:

J.Tame,A.J.Wilkinson

Key ref:

J.R.Tame et al. (1996). The role of water in sequence-independent ligand binding by an oligopeptide transporter protein. Nat Struct Biol, 3, 998. PubMed id: 8946852

Date:

03-Jul-96

Release date:

15-May-97

PROCHECK

	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:

PfamA domain

Secondary structure

CATH domain

	Nat Struct Biol 3:998 (1996)
PubMed id: 8946852

The role of water in sequence-independent ligand binding by an oligopeptide transporter protein.
J.R.Tame, S.H.Sleigh, A.J.Wilkinson, J.E.Ladbury.

ABSTRACT

No abstract given.

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.

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.

21131908

S.Newstead, D.Drew, A.D.Cameron, V.L.Postis, X.Xia, P.W.Fowler, J.C.Ingram, E.P.Carpenter, M.S.Sansom, M.J.McPherson, S.A.Baldwin, and S.Iwata (2011).
Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2.

EMBO J, 30, 417-426.

PDB code:

2xut

20345171

C.Bissantz, B.Kuhn, and M.Stahl (2010).
A medicinal chemist's guide to molecular interactions.

J Med Chem, 53, 5061-5084.

20711360

D.J.Huggins, G.J.McKenzie, D.D.Robinson, A.J.Narváez, B.Hardwick, M.Roberts-Thomson, A.R.Venkitaraman, G.H.Grant, and M.C.Payne (2010).
Computational analysis of phosphopeptide binding to the polo-box domain of the mitotic kinase PLK1 using molecular dynamics simulation.

PLoS Comput Biol, 6, 0.

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

19300437

R.P.Berntsson, M.K.Doeven, F.Fusetti, R.H.Duurkens, D.Sengupta, S.J.Marrink, A.M.Thunnissen, B.Poolman, and D.J.Slotboom (2009).
The structural basis for peptide selection by the transport receptor OppA.

EMBO J, 28, 1332-1340.

PDB codes:

3drf 3drg 3drh 3dri 3drj 3drk

18465087

P.Arun Prasad, and N.Gautham (2008).
A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling.

J Comput Aided Mol Des, 22, 815-829.

17443320

G.Bruylants, R.Wintjens, Y.Looze, C.Redfield, and K.Bartik (2007).
Protonation linked equilibria and apparent affinity constants: the thermodynamic profile of the alpha-chymotrypsin-proflavin interaction.

Eur Biophys J, 37, 11-18.

17372351

K.Fukuyama, and T.Okada (2007).
Structures of cyanide, nitric oxide and hydroxylamine complexes of Arthromyces ramosusperoxidase at 100 K refined to 1.3 A resolution: coordination geometries of the ligands to the haem iron.

Acta Crystallogr D Biol Crystallogr, 63, 472-477.

PDB codes:

2e39 2e3a 2e3b

16899489

A.D.van Dijk, and A.M.Bonvin (2006).
Solvated docking: introducing water into the modelling of biomolecular complexes.

Bioinformatics, 22, 2340-2347.

16489544

R.Andersen, F.S.Jørgensen, L.Olsen, J.Våbenø, K.Thorn, C.U.Nielsen, and B.Steffansen (2006).
Development of a QSAR model for binding of tripeptides and tripeptidomimetics to the human intestinal di-/tripeptide transporter hPEPT1.

Pharm Res, 23, 483-492.

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.

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

12960164

J.Heddle, D.J.Scott, S.Unzai, S.Y.Park, and J.R.Tame (2003).
Crystal structures of the liganded and unliganded nickel-binding protein NikA from Escherichia coli.

J Biol Chem, 278, 50322-50329.

PDB codes:

1uiu 1uiv

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.

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.

10692365

A.Picon, E.R.Kunji, F.C.Lanfermeijer, W.N.Konings, and B.Poolman (2000).
Specificity mutants of the binding protein of the oligopeptide transport system of Lactococcus lactis.

J Bacteriol, 182, 1600-1608.

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.

10662684

J.E.Ladbury, and S.Arold (2000).
Searching for specificity in SH domains.

Chem Biol, 7, R3-R8.

11208110

P.Luan, A.Heine, K.Zeng, B.Moyer, S.E.Greasely, P.Kuhn, W.E.Balch, and I.A.Wilson (2000).
A new functional domain of guanine nucleotide dissociation inhibitor (alpha-GDI) involved in Rab recycling.

Traffic, 1, 270-281.

PDB code:

1d5t

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.

10422831

T.G.Davies, R.E.Hubbard, and J.R.Tame (1999).
Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes.

Protein Sci, 8, 1432-1444.

PDB codes:

1b0h 1b1h 1b2h 1b3h 1b4h 1b5h 1b6h 1b7h

9753693

E.Chung, D.Henriques, D.Renzoni, M.Zvelebil, J.M.Bradshaw, G.Waksman, C.V.Robinson, and J.E.Ladbury (1998).
Mass spectrometric and thermodynamic studies reveal the role of water molecules in complexes formed between SH2 domains and tyrosyl phosphopeptides.

Structure, 6, 1141-1151.

9914254

S.Longhi, M.Czjzek, and C.Cambillau (1998).
Messages from ultrahigh resolution crystal structures.

Curr Opin Struct Biol, 8, 730-737.

9278422

M.A.Schumacher, A.Glasfeld, H.Zalkin, and R.G.Brennan (1997).
The X-ray structure of the PurR-guanine-purF operator complex reveals the contributions of complementary electrostatic surfaces and a water-mediated hydrogen bond to corepressor specificity and binding affinity.

J Biol Chem, 272, 22648-22653.

PDB code:

1wet

9309218

R.Tyrrell, K.H.Verschueren, E.J.Dodson, G.N.Murshudov, C.Addy, and A.J.Wilkinson (1997).
The structure of the cofactor-binding fragment of the LysR family member, CysB: a familiar fold with a surprising subunit arrangement.

Structure, 5, 1017-1032.

PDB code:

1al3

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

9000013

J.E.Ladbury (1996).
Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design.

Chem Biol, 3, 973-980.

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 code is shown on the right.