PDBsum entry 2lbp

Periplasmic binding protein

PDB id

2lbp

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Contents

			Protein chain

					346 a.a. *

			Waters ×91

* Residue conservation analysis

PDB id:

2lbp

Links

Name:

Periplasmic binding protein

Title:

Structure of the l-leucine-binding protein refined at 2.4 angstroms resolution and comparison with the leu(slash)ile(slash)val-binding protein structure

Structure:

Leucine-binding protein. Chain: a. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562.

Resolution:

2.40Å

R-factor:

0.213

Authors:

J.S.Sack,S.D.Trakhanov,I.H.Tsigannik,F.A.Quiocho

Key ref:

J.S.Sack et al. (1989). Structure of the L-leucine-binding protein refined at 2.4 A resolution and comparison with the Leu/Ile/Val-binding protein structure. J Mol Biol, 206, 193-207. PubMed id: 2649683

Date:

10-Apr-89

Release date:

12-Jul-89

PROCHECK

	Headers

	References

Protein chain

P04816 (LIVK_ECOLI) - Leucine-specific-binding protein from Escherichia coli (strain K12)

Seq: Struc:					369 a.a. 346 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

	J Mol Biol 206:193-207 (1989)
PubMed id: 2649683

Structure of the L-leucine-binding protein refined at 2.4 A resolution and comparison with the Leu/Ile/Val-binding protein structure.
J.S.Sack, S.D.Trakhanov, I.H.Tsigannik, F.A.Quiocho.

ABSTRACT

The three-dimensional X-ray structure of the leucine-binding protein (36,900 Mr and 346 residues), an active transport component of Escherichia coli, has been determined by the method of molecular replacement, using the refined structure of the Leu/Ile/Val-binding protein (344 residues) as the model structure. The two amino acid-binding proteins have 80% sequence identity and, although both crystallize in the same space group, they have very different unit cell dimensions. The rotation function yielded one significant peak, which subsequently led to a single self-consistent translation function solution. The model was first refined by the constrained least-squares method, with each of the two domains of the molecule treated separately to allow for any small change in the relative orientation of the two domains. The model was then modified in order to reflect the 72 changes in amino acid side-chains and two insertions in going from the Leu/Ile/Val-binding protein sequence to that of the L-leucine-binding protein. Final structure refinement, using the restrained least-squares technique, resulted in an R-factor of 0.20 for 13,797 reflections to a resolution of 2.4 A. The model is comprised of 2600 protein atoms and 91 solvent molecules. The L-leucine-binding protein structure is, as expected, very similar to the Leu/Ile/Val-binding protein structure; both are in the unliganded conformation with the cleft between the two domains wide open and easily accessible. The superimposing of the structures yields a root-mean-square difference of 0.68 A in the alpha-carbon atoms of the 317 equivalent residues. The five regions of the leucine-binding protein structure that differ by more than 1.6 A from the Leu/Ile/Val-binding protein structure are far from the major portion of the ligand-binding site, which is located in one domain of the bilobate protein. Between the structures, there are three differences in the amino acid side-chains that form the major portion of the substrate-binding sites. These substitutions, by themselves, fail to clearly explain the differences in the specificities for branched aliphatic amino acids.

Literature references that cite this PDB file's key reference

PubMed id

Reference

19643201

K.Igarashi, and K.Kashiwagi (2010).
Modulation of cellular function by polyamines.

Int J Biochem Cell Biol, 42, 39-51.

19348466

M.J.Borrok, Y.Zhu, K.T.Forest, and L.L.Kiessling (2009).
Structure-based design of a periplasmic binding protein antagonist that prevents domain closure.

ACS Chem Biol, 4, 447-456.

PDB code:

2qw1

18509460

R.D.Emes, and Z.Yang (2008).
Duplicated paralogous genes subject to positive selection in the genome of Trypanosoma brucei.

PLoS ONE, 3, e2295.

19052373

S.Moréra, V.Gueguen-Chaignon, A.Raffoux, and D.Faure (2008).
Cloning, purification, crystallization and preliminary X-ray analysis of a bacterial GABA receptor with a Venus flytrap fold.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1153-1155.

17927700

A.Garcia-Herrero, R.S.Peacock, S.P.Howard, and H.J.Vogel (2007).
The solution structure of the periplasmic domain of the TonB system ExbD protein reveals an unexpected structural homology with siderophore-binding proteins.

Mol Microbiol, 66, 872-889.

PDB code:

2pfu

17473016

M.J.Borrok, L.L.Kiessling, and K.T.Forest (2007).
Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-high-resolution ligand-bound structures.

Protein Sci, 16, 1032-1041.

PDB codes:

2fvy 2fw0

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.

15388932

H.Takahashi, E.Inagaki, C.Kuroishi, and T.H.Tahirov (2004).
Structure of the Thermus thermophilus putative periplasmic glutamate/glutamine-binding protein.

Acta Crystallogr D Biol Crystallogr, 60, 1846-1854.

PDB codes:

1us4 1us5

14672931

U.Magnusson, B.Salopek-Sondi, L.A.Luck, and S.L.Mowbray (2004).
X-ray structures of the leucine-binding protein illustrate conformational changes and the basis of ligand specificity.

J Biol Chem, 279, 8747-8752.

PDB codes:

1usg 1usi 1usk

14517978

B.Salopek-Sondi, M.C.Skeels, D.Swartz, and L.A.Luck (2003).
Insight into the stability of the hydrophobic binding proteins of Escherichia coli: assessing the proteins for use as biosensors.

Proteins, 53, 273-281.

14611761

L.A.Luck, M.J.Moravan, J.E.Garland, B.Salopek-Sondi, and D.Roy (2003).
Chemisorptions of bacterial receptors for hydrophobic amino acids and sugars on gold for biosensor applications: a surface plasmon resonance study of genetically engineered proteins.

Biosens Bioelectron, 19, 249-259.

11844750

A.L.Davidson (2002).
Mechanism of coupling of transport to hydrolysis in bacterial ATP-binding cassette transporters.

J Bacteriol, 184, 1225-1233.

11152130

A.S.Bessis, H.O.Bertrand, T.Galvez, C.De Colle, J.P.Pin, and F.Acher (2000).
Three-dimensional model of the extracellular domain of the type 4a metabotropic glutamate receptor: new insights into the activation process.

Protein Sci, 9, 2200-2209.

10986237

C.Sprencel, Z.Cao, Z.Qi, D.C.Scott, M.A.Montague, N.Ivanoff, J.Xu, K.M.Raymond, S.M.Newton, and P.E.Klebba (2000).
Binding of ferric enterobactin by the Escherichia coli periplasmic protein FepB.

J Bacteriol, 182, 5359-5364.

11206079

L.A.Luck, and C.Johnson (2000).
Fluorescence and 19F NMR evidence that phenylalanine, 3-L-fluorophenylalanine and 4-L-fluorophenylalanine bind to the L-leucine specific receptor of Escherichia coli.

Protein Sci, 9, 2573-2576.

11086992

N.Armstrong, and E.Gouaux (2000).
Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: crystal structures of the GluR2 ligand binding core.

Neuron, 28, 165-181.

PDB codes:

1ftj 1ftk 1ftl 1ftm 1fto 1fw0

10733987

O.Keskin, R.L.Jernigan, and I.Bahar (2000).
Proteins with similar architecture exhibit similar large-scale dynamic behavior.

Biophys J, 78, 2093-2106.

11163276

P.Paoletti, F.Perin-Dureau, A.Fayyazuddin, A.Le Goff, I.Callebaut, and J.Neyton (2000).
Molecular organization of a zinc binding n-terminal modulatory domain in a NMDA receptor subunit.

Neuron, 28, 911-925.

10224098

T.Galvez, M.L.Parmentier, C.Joly, B.Malitschek, K.Kaupmann, R.Kuhn, H.Bittiger, W.Froestl, B.Bettler, and J.P.Pin (1999).
Mutagenesis and modeling of the GABAB receptor extracellular domain support a venus flytrap mechanism for ligand binding.

J Biol Chem, 274, 13362-13369.

9651355

D.G.Vassylyev, H.Tomitori, K.Kashiwagi, K.Morikawa, and K.Igarashi (1998).
Crystal structure and mutational analysis of the Escherichia coli putrescine receptor. Structural basis for substrate specificity.

J Biol Chem, 273, 17604-17609.

PDB code:

1a99

9582347

T.Okamoto, N.Sekiyama, M.Otsu, Y.Shimada, A.Sato, S.Nakanishi, and H.Jingami (1998).
Expression and purification of the extracellular ligand binding region of metabotropic glutamate receptor subtype 1.

J Biol Chem, 273, 13089-13096.

9201949

D.Chamberlain, B.P.O'Hara, S.A.Wilson, L.H.Pearl, and S.J.Perkins (1997).
Oligomerization of the amide sensor protein AmiC by x-ray and neutron scattering and molecular modeling.

Biochemistry, 36, 8020-8029.

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

8861200

F.A.Quiocho, and P.S.Ledvina (1996).
Atomic structure and specificity of bacterial periplasmic receptors for active transport and chemotaxis: variation of common themes.

Mol Microbiol, 20, 17-25.

8897598

S.Sugiyama, Y.Matsuo, K.Maenaka, D.G.Vassylyev, M.Matsushima, K.Kashiwagi, K.Igarashi, and K.Morikawa (1996).
The 1.8-A X-ray structure of the Escherichia coli PotD protein complexed with spermidine and the mechanism of polyamine binding.

Protein Sci, 5, 1984-1990.

PDB code:

1pot

8749853

D.Frishman, and P.Argos (1995).
Knowledge-based protein secondary structure assignment.

Proteins, 23, 566-579.

8747465

J.R.Tame, E.J.Dodson, G.Murshudov, C.F.Higgins, and A.J.Wilkinson (1995).
The crystal structures of the oligopeptide-binding protein OppA complexed with tripeptide and tetrapeptide ligands.

Structure, 3, 1395-1406.

PDB codes:

1olc 2olb

8528088

S.Trakhanov, and F.A.Quiocho (1995).
Influence of divalent cations in protein crystallization.

Protein Sci, 4, 1914-1919.

8062817

A.Vrielink, W.Rüger, H.P.Driessen, and P.S.Freemont (1994).
Crystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose.

EMBO J, 13, 3413-3422.

PDB codes:

1bgt 1bgu 2bgt 2bgu

8035212

S.D.Rufino, and T.L.Blundell (1994).
Structure-based identification and clustering of protein families and superfamilies.

J Comput Aided Mol Des, 8, 5.

7703851

Y.Matsuo, and K.Nishikawa (1994).
Protein structural similarities predicted by a sequence-structure compatibility method.

Protein Sci, 3, 2055-2063.

8338667

P.J.O'Hara, P.O.Sheppard, H.Thøgersen, D.Venezia, B.A.Haldeman, V.McGrane, K.M.Houamed, C.Thomsen, T.L.Gilbert, and E.R.Mulvihill (1993).
The ligand-binding domain in metabotropic glutamate receptors is related to bacterial periplasmic binding proteins.

Neuron, 11, 41-52.

1757475

M.D.Adams, and D.L.Oxender (1991).
Secretion of mutant leucine-specific binding proteins with internal deletions in Escherichia coli.

J Cell Biochem, 46, 321-330.

2191293

R.M.Williamson, and D.L.Oxender (1990).
Sequence and structural similarities between the leucine-specific binding protein and leucyl-tRNA synthetase of Escherichia coli.

Proc Natl Acad Sci U S A, 87, 4561-4565.

2771945

P.Van Roey, and T.A.Beerman (1989).
Crystal structure analysis of auromomycin apoprotein (macromomycin) shows importance of protein side chains to chromophore binding selectivity.

Proc Natl Acad Sci U S A, 86, 6587-6591.

PDB code:

2mcm

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.