1O94

Ternary complex between trimethylamine dehydrogenase and electron transferring flavoprotein

PDB DOI: https://doi.org/10.2210/pdb1O94/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Methylophilus methylotrophus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2002-12-11 Released: 2003-02-06
Deposition Author(s): Leys, D., Basran, J., Talfournier, F., Sutcliffe, M.J., Scrutton, N.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.212
R-Value Work: 0.172
R-Value Observed: 0.174

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Extensive Conformational Sampling in a Ternary Electron Transfer Complex.

Leys, D., Basran, J., Talfournier, F., Sutcliffe, M.J., Scrutton, N.S.

(2003) Nat Struct Biol 10: 219

PubMed: 12567183 Search on PubMed
DOI: https://doi.org/10.1038/nsb894
Primary Citation of Related Structures:
1O94, 1O95, 1O96, 1O97

PubMed Abstract:
Here we report the crystal structures of a ternary electron transfer complex showing extensive motion at the protein interface. This physiological complex comprises the iron-sulfur flavoprotein trimethylamine dehydrogenase and electron transferring flavoprotein (ETF) from Methylophilus methylotrophus. In addition, we report the crystal structure of free ETF. In the complex, electron density for the FAD domain of ETF is absent, indicating high mobility. Positions for the FAD domain are revealed by molecular dynamics simulation, consistent with crystal structures and kinetic data. A dual interaction of ETF with trimethylamine dehydrogenase provides for dynamical motion at the protein interface: one site acts as an anchor, thereby allowing the other site to sample a large range of interactions, some compatible with rapid electron transfer. This study establishes the role of conformational sampling in multi-domain redox systems, providing insight into electron transfer between ETFs and structurally distinct redox partners.

Organizational Affiliation

Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, UK. [email protected]

Macromolecule Content

Total Structure Weight: 291.48 kDa
Atom Count: 19,925
Modelled Residue Count: 2,305
Deposited Residue Count: 2,626
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRIMETHYLAMINE DEHYDROGENASE	A, B	729	Methylophilus methylotrophus	Mutation(s): 0 EC: 1.5.99.7 (PDB Primary Data), 1.5.8.2 (UniProt)
UniProt
Find proteins for P16099 (Methylophilus methylotrophus) Explore P16099 Go to UniProtKB: P16099
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16099
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ELECTRON TRANSFER FLAVOPROTEIN BETA-SUBUNIT	C, E	264	Methylophilus methylotrophus	Mutation(s): 0
UniProt
Find proteins for P53570 (Methylophilus methylotrophus) Explore P53570 Go to UniProtKB: P53570
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53570
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ELECTRON TRANSFER FLAVOPROTEIN ALPHA-SUBUNIT	D, F	320	Methylophilus methylotrophus	Mutation(s): 0
UniProt
Find proteins for P53571 (Methylophilus methylotrophus) Explore P53571 Go to UniProtKB: P53571
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53571
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	G [auth A], J [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B]	H [auth A], K [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B]	I [auth A], L [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B]
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain N [auth E] MOL2 format, chain M [auth C] MOL2 format, chain N [auth E] mmCIF format, chain M [auth C] mmCIF format, chain N [auth E]	M [auth C], N [auth E]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain M [auth C] Focus chain N [auth E] Interactions & Density Focus chain M [auth C] Focus chain N [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.212
R-Value Work: 0.172
R-Value Observed: 0.174
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.93	α = 90
b = 211.543	β = 100.03
c = 125.97	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-02-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-02-06
Type: Initial release
Version 1.1: 2013-09-18
Changes: Derived calculations, Non-polymer description, Other, Version format compliance
Version 1.2: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary