Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C6  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.69 kDa 
• Atom Count: 4415 
• Modelled Residue Count: 509 
• Deposited Residue Count: 519 
• Unique protein chains: 1

3O9P

The structure of the Escherichia coli murein tripeptide binding protein MppA

• PDB DOI: 10.2210/pdb3O9P/pdb

• Classification: PEPTIDE BINDING PROTEIN/PEPTIDE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-08-04 Released: 2011-07-06 
• Deposition Author(s): Maqbool, A., Levdikov, V.M., Blagova, E.V., Wilkinson, A.J., Thomas, G.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.218 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Literature

Compensating Stereochemical Changes Allow Murein Tripeptide to Be Accommodated in a Conventional Peptide-binding Protein.

Maqbool, A., Levdikov, V.M., Blagova, E.V., Herve, M., Horler, R.S., Wilkinson, A.J., Thomas, G.H.

(2011) J Biol Chem 286: 31512-31521

• PubMed: 21705338 
• DOI: 10.1074/jbc.M111.267179
• Primary Citation of Related Structures:  
  3O9P


• PubMed Abstract: 
  

The oligopeptide permease (Opp) of Escherichia coli is an ATP-binding cassette transporter that uses the substrate-binding protein (SBP) OppA to bind peptides and deliver them to the membrane components (OppBCDF) for transport. OppA binds conventional peptides 2-5 residues in length regardless of their sequence, but does not facilitate transport of the cell wall component murein tripeptide (Mtp, L-Ala-γ-D-Glu-meso-Dap), which contains a D-amino acid and a γ-peptide linkage. Instead, MppA, a homologous substrate-binding protein, forms a functional transporter with OppBCDF for uptake of this unusual tripeptide. Here we have purified MppA and demonstrated biochemically that it binds Mtp with high affinity (K(D) ∼ 250 nM). The crystal structure of MppA in complex with Mtp has revealed that Mtp is bound in a relatively extended conformation with its three carboxylates projecting from one side of the molecule and its two amino groups projecting from the opposite face. Specificity for Mtp is conferred by charge-charge and dipole-charge interactions with ionic and polar residues of MppA. Comparison of the structure of MppA-Mtp with structures of conventional tripeptides bound to OppA, reveals that the peptide ligands superimpose remarkably closely given the profound differences in their structures. Strikingly, the effect of the D-stereochemistry, which projects the side chain of the D-Glu residue at position 2 in the direction of the main chain in a conventional tripeptide, is compensated by the formation of a γ-linkage to the amino group of diaminopimelic acid, mimicking the peptide bond between residues 2 and 3 of a conventional tripeptide.

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Organizational Affiliation: 

Department of Biology (Area 10), University of York, York YO10 5YW, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic murein peptide-binding protein	A	519	Escherichia coli	Mutation(s): 0  Gene Names: b1329, JW1322, mppA, ynaH
UniProt
Find proteins for P77348 (Escherichia coli (strain K12)) Explore P77348  Go to UniProtKB:  P77348

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MHI	B [auth A]	L-ALA-GAMMA-D-GLU-MESO-DIAMINOPIMELIC ACID C15 H26 N4 O8 FMNCPUGORYYCEM-QCLAVDOMSA-N
ZN	C [auth A], D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MHI	Binding MOAD:  3O9P	Kd: 300 (nM) from 1 assay(s)
	PDBBind:  3O9P	Kd: 300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.218 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.074	α = 90
b = 165.074	β = 90
c = 38.167	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-08-04 
• Released Date: 2011-07-06 
Deposition Author(s): Maqbool, A., Levdikov, V.M., Blagova, E.V., Wilkinson, A.J., Thomas, G.H.

Revision History  

• Version 1.0: 2011-07-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-09-14
  Changes: Database references
• Version 1.3: 2011-09-21
  Changes: Database references