4R9U

Structure of vitamin B12 transporter BtuCD in a nucleotide-bound outward facing state

PDB DOI: https://doi.org/10.2210/pdb4R9U/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2014-09-08 Released: 2014-11-19
Deposition Author(s): Korkhov, V.M., Mireku, S.A., Veprintsev, D.B., Locher, K.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.246
R-Value Work: 0.217
R-Value Observed: 0.218

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of AMP-PNP-bound BtuCD and mechanism of ATP-powered vitamin B12 transport by BtuCD-F.

Korkhov, V.M., Mireku, S.A., Veprintsev, D.B., Locher, K.P.

(2014) Nat Struct Mol Biol 21: 1097-1099

PubMed: 25402482 Search on PubMed
DOI: https://doi.org/10.1038/nsmb.2918
Primary Citation of Related Structures:
4R9U

PubMed Abstract:
The reaction mechanism of BtuCD-F-catalyzed vitamin B12 transport into Escherichia coli is currently unclear. Here we present the structure of the last missing state in the form of AMP-PNP-bound BtuCD, trapped by a disulfide cross-link. Our structural and biochemical data allow a consistent mechanism to be formulated, thus rationalizing the roles of substrate, ATP and substrate-binding protein.

Organizational Affiliation

1] Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland. [2] Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland.

Macromolecule Content

Total Structure Weight: 127.12 kDa
Atom Count: 8,792
Modelled Residue Count: 1,144
Deposited Residue Count: 1,164
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin B12 import system permease protein BtuC	A, B	333	Escherichia coli K-12	Mutation(s): 7 Gene Names: btuC, b1711, JW1701 EC: 3.6.3.33 Membrane Entity: Yes
UniProt
Find proteins for P06609 (Escherichia coli (strain K12)) Explore P06609 Go to UniProtKB: P06609
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06609
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin B12 import ATP-binding protein BtuD	C, D	249	Escherichia coli K-12	Mutation(s): 3 Gene Names: btuD, b1709, JW1699 EC: 3.6.3.33 Membrane Entity: Yes
UniProt
Find proteins for P06611 (Escherichia coli (strain K12)) Explore P06611 Go to UniProtKB: P06611
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06611
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D]	I [auth C], K [auth D]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain I [auth C] Focus chain K [auth D]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A]	E [auth A], F [auth A], G [auth B], H [auth B]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D]	J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.246
R-Value Work: 0.217
R-Value Observed: 0.218
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 372.85	α = 90
b = 113.21	β = 94.92
c = 69.43	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-11-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-19
Type: Initial release
Version 1.1: 2014-12-03
Changes: Database references
Version 1.2: 2014-12-17
Changes: Database references
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description