4DBL | pdb_00004dbl

Crystal structure of E159Q mutant of BtuCDF

PDB DOI: https://doi.org/10.2210/pdb4DBL/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2012-01-16 Released: 2012-03-07
Deposition Author(s): Korkhov, V.M., Mireku, S.M., Hvorup, R.N., Locher, K.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.49 Å
R-Value Free:
0.251 (Depositor), 0.244 (DCC)
R-Value Work:
0.214 (Depositor), 0.207 (DCC)
R-Value Observed:
0.215 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Asymmetric states of vitamin B12 transporter BtuCD are not discriminated by its cognate substrate binding protein BtuF.

Korkhov, V.M., Mireku, S.A., Hvorup, R.N., Locher, K.P.

(2012) FEBS Lett 586: 972-976

PubMed: 22569249 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2012.02.042
Primary Citation Related Structures:
4DBL

PubMed Abstract:
BtuCD is an ABC transporter catalyzing the uptake of vitamin B₁₂ across the Escherichia coli inner membrane. A previously reported X-ray structure of BtuCD in complex with the periplasmic vitamin B₁₂-binding protein BtuF revealed asymmetry of the transmembrane BtuC subunits. The functional relevance of this asymmetry has remained uncertain. Here we report the X-ray structure of a catalytically impaired BtuCD mutant in complex with BtuF, where the BtuC subunits adopt a distinct asymmetric conformation. The structure suggests that BtuF does not discriminate between, or impose, asymmetric conformations of BtuCD. It also explains the conformational disorder observed in BtuCDF crystals.

Organizational Affiliation

Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Switzerland.

Macromolecule Content

Total Structure Weight: 317 kDa
Atom Count: 21,230
Modeled Residue Count: 2,778
Deposited Residue Count: 2,902
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin B12 import system permease protein BtuC	A, B, F, G	349	Escherichia coli K-12	Mutation(s): 7 Membrane Entity: Yes
UniProt
Find proteins for P06609 (Escherichia coli (strain K12)) Explore P06609 Go to UniProtKB: P06609
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06609
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin B12 import ATP-binding protein BtuD	C, D, H, I	249	Escherichia coli K-12	Mutation(s): 2 EC: 3.6.3.33 (PDB Primary Data), 7.6.2.8 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P06611 (Escherichia coli (strain K12)) Explore P06611 Go to UniProtKB: P06611
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06611
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin B12-binding protein	E, J	255	Escherichia coli K-12	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P37028 (Escherichia coli (strain K12)) Explore P37028 Go to UniProtKB: P37028
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P37028
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth I] SDF format, chain Y [auth I] SDF format, chain X [auth I] SDF format, chain V [auth H] SDF format, chain U [auth H] SDF format, chain T [auth H] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth C] MOL2 format, chain Z [auth I] MOL2 format, chain Y [auth I] MOL2 format, chain X [auth I] MOL2 format, chain V [auth H] MOL2 format, chain U [auth H] MOL2 format, chain T [auth H] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] mmCIF format, chain Z [auth I] mmCIF format, chain Y [auth I] mmCIF format, chain X [auth I] mmCIF format, chain V [auth H] mmCIF format, chain U [auth H] mmCIF format, chain T [auth H] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C]	L [auth C] M [auth C] N [auth C] P [auth D] Q [auth D] L [auth C], M [auth C], N [auth C], P [auth D], Q [auth D], R [auth D], T [auth H], U [auth H], V [auth H], X [auth I], Y [auth I], Z [auth I]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth H] Focus chain U [auth H] Focus chain V [auth H] Focus chain X [auth I] Focus chain Y [auth I] Focus chain Z [auth I] Interactions & Density Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth H] Focus chain U [auth H] Focus chain V [auth H] Focus chain X [auth I] Focus chain Y [auth I] Focus chain Z [auth I]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain W [auth I] SDF format, chain S [auth H] SDF format, chain O [auth D] SDF format, chain K [auth C] MOL2 format, chain W [auth I] MOL2 format, chain S [auth H] MOL2 format, chain O [auth D] MOL2 format, chain K [auth C] mmCIF format, chain W [auth I] mmCIF format, chain S [auth H] mmCIF format, chain O [auth D] mmCIF format, chain K [auth C]	K [auth C], O [auth D], S [auth H], W [auth I]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain K [auth C] Focus chain O [auth D] Focus chain S [auth H] Focus chain W [auth I] Interactions & Density Focus chain K [auth C] Focus chain O [auth D] Focus chain S [auth H] Focus chain W [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.49 Å
R-Value Free: 0.251 (Depositor), 0.244 (DCC)
R-Value Work: 0.214 (Depositor), 0.207 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.65	α = 90
b = 166.93	β = 119.76
c = 132.82	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
PHENIX	model building
PHENIX	refinement
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-03-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-03-07
Type: Initial release
Version 1.1: 2012-05-23
Changes: Database references
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary