3EFP | pdb_00003efp

Crystal structure of the Escherichia coli twin arginine leader peptide binding protein DmsD in a monomeric form

PDB DOI: https://doi.org/10.2210/pdb3EFP/pdb

Classification: CHAPERONE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-09 Released: 2009-04-07
Deposition Author(s): Stevens, C.M., Paetzel, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.213 (Depositor), 0.212 (DCC)
R-Value Work:
0.178 (Depositor), 0.179 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural analysis of a monomeric form of the twin-arginine leader peptide binding chaperone Escherichia coli DmsD.

Stevens, C.M., Winstone, T.M., Turner, R.J., Paetzel, M.

(2009) J Mol Biology 389: 124-133

PubMed: 19361518 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jmb.2009.03.069
Primary Citation Related Structures:
3EFP

PubMed Abstract:
The redox enzyme maturation proteins play an essential role in the proofreading and membrane targeting of protein substrates to the twin-arginine translocase. Functionally, the most thoroughly characterized redox enzyme maturation protein to date is Escherichia coli DmsD (EcDmsD). Herein, we present the X-ray crystal structure of the monomeric form of the EcDmsD refined to 2.0 A resolution, with clear electron density present for each of its 204 amino acid residues. The structural data presented here complement the biochemical data previously generated regarding the function of these twin-arginine translocase leader peptide binding chaperone proteins. Docking and molecular dynamics simulation experiments were used to provide a proposed model for how this chaperone is able to recognize the leader peptide of its substrate DmsA. The interactions observed in the model are in agreement with previous biochemical data and suggest intimate interactions between the conserved twin-arginine motif of the leader peptide of E. coli DmsA and the most conserved regions on the surface of EcDmsD.

Organizational Affiliation

Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.

Macromolecule Content

Total Structure Weight: 48.98 kDa
Atom Count: 3,860
Modeled Residue Count: 412
Deposited Residue Count: 416
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Twin-arginine leader-binding protein dmsD	A, B	208	Escherichia coli K-12	Mutation(s): 0 Gene Names: dmsD, ynfI, b1591, JW5262
UniProt
Find proteins for P69853 (Escherichia coli (strain K12)) Explore P69853 Go to UniProtKB: P69853
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69853
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain E [auth A]	C [auth A], E [auth A], M [auth B], N [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain M [auth B] Focus chain N [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain O [auth B] SDF format, chain G [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth B] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A]	D [auth A] F [auth A] G [auth A] H [auth A] L [auth B] D [auth A], F [auth A], G [auth A], H [auth A], L [auth B], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain J [auth A]	I [auth A] J [auth A] K [auth A] P [auth B] Q [auth B] I [auth A], J [auth A], K [auth A], P [auth B], Q [auth B], R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.213 (Depositor), 0.212 (DCC)
R-Value Work: 0.178 (Depositor), 0.179 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.02	α = 90
b = 128.02	β = 90
c = 78.723	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-04-07

Deposition Author(s):

Stevens, C.M.

Paetzel, M.

Revision History (Full details and data files)

Version 1.0: 2009-04-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description