6B58 | pdb_00006b58

FrdA-SdhE assembly intermediate

• PDB DOI: https://doi.org/10.2210/pdb6B58/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-09-28 Released: 2018-01-24 
• Deposition Author(s): Sharma, P., Iverson, T.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Veterans Affairs

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 
  0.255 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an assembly intermediate of respiratory Complex II.

Sharma, P., Maklashina, E., Cecchini, G., Iverson, T.M.

(2018) Nat Commun 9: 274-274

• PubMed: 29348404 
• DOI: https://doi.org/10.1038/s41467-017-02713-8
• Primary Citation Related Structures: 
  6B58


• PubMed Abstract: 
  

  Flavin is covalently attached to the protein scaffold in ~10% of flavoenzymes. However, the mechanism of covalent modification is unclear, due in part to challenges in stabilizing assembly intermediates. Here, we capture the structure of an assembly intermediate of the Escherichia coli Complex II (quinol:fumarate reductase (FrdABCD)). The structure contains the E. coli FrdA subunit bound to covalent FAD and crosslinked with its assembly factor, SdhE. The structure contains two global conformational changes as compared to prior structures of the mature protein: the rotation of a domain within the FrdA subunit, and the destabilization of two large loops of the FrdA subunit, which may create a tunnel to the active site. We infer a mechanism for covalent flavinylation. As supported by spectroscopic and kinetic analyses, we suggest that SdhE shifts the conformational equilibrium of the FrdA active site to disfavor succinate/fumarate interconversion and enhance covalent flavinylation.

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Organizational Affiliation: 
• Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA.
Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, 94121, USA.
Department of Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA.
Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, 94121, USA. [e-mail].
Department of Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA. [e-mail].
Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA. [e-mail].
Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA. [e-mail].
Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA. [e-mail].
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37232, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: cross-linking

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 149.18 kDa 
• Atom Count: 9,567 
• Modeled Residue Count: 1,243 
• Deposited Residue Count: 1,312 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fumarate reductase flavoprotein subunit	A, C	577	Escherichia coli	Mutation(s): 0  EC: 1.3.5.4 (PDB Primary Data), 1.3.5.1 (UniProt)
UniProt
Find proteins for P00363 (Escherichia coli (strain K12)) Explore P00363  Go to UniProtKB:  P00363

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD assembly factor SdhE	B, D	79	Escherichia coli	Mutation(s): 1
UniProt
Find proteins for P64559 (Escherichia coli (strain K12)) Explore P64559  Go to UniProtKB:  P64559

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], R [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PEG	T [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MLI	U [auth C]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
GOL	V [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	N [auth A], O [auth A], P [auth A], Q [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], W [auth C], X [auth C], Y [auth C], Z [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
K	F [auth A], S [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PBF	B, D	L-PEPTIDE LINKING	C16 H15 N O3		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free:  0.255 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.64	α = 90
b = 63.33	β = 96.83
c = 175.58	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-24 
Deposition Author(s): Sharma, P., Iverson, T.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM061606
Department of Veterans Affairs	United States	BX001077

Revision History  

• Version 1.0: 2018-01-24
  Type: Initial release
  
• Version 1.1: 2018-01-31
  Changes: Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection