2WP9 | pdb_00002wp9

Crystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhB His207Thr mutant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.222 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history. 

Literature

Perturbation of the quinone-binding site of complex II alters the electronic properties of the proximal [3Fe-4S] iron-sulfur cluster.

Ruprecht, J., Iwata, S., Rothery, R.A., Weiner, J.H., Maklashina, E., Cecchini, G.

(2011) J Biological Chem 286: 12756-12765

  • DOI: https://doi.org/10.1074/jbc.M110.209874
  • Primary Citation Related Structures: 
    2WP9

  • PubMed Abstract: 

    Succinate-ubiquinone oxidoreductase (SQR) and menaquinol-fumarate oxidoreductase (QFR) from Escherichia coli are members of the complex II family of enzymes. SQR and QFR catalyze similar reactions with quinones; however, SQR preferentially reacts with higher potential ubiquinones, and QFR preferentially reacts with lower potential naphthoquinones. Both enzymes have a single functional quinone-binding site proximal to a [3Fe-4S] iron-sulfur cluster. A difference between SQR and QFR is that the redox potential of the [3Fe-4S] cluster in SQR is 140 mV higher than that found in QFR. This may reflect the character of the different quinones with which the two enzymes preferentially react. To investigate how the environment around the [3Fe-4S] cluster affects its redox properties and catalysis with quinones, a conserved amino acid proximal to the cluster was mutated in both enzymes. It was found that substitution of SdhB His-207 by threonine (as found in QFR) resulted in a 70-mV lowering of the redox potential of the cluster as measured by EPR. The converse substitution in QFR raised the redox potential of the cluster. X-ray structural analysis suggests that placing a charged residue near the [3Fe-4S] cluster is a primary reason for the alteration in redox potential with the hydrogen bonding environment having a lesser effect. Steady state enzyme kinetic characterization of the mutant enzymes shows that the redox properties of the [3Fe-4S] cluster have only a minor effect on catalysis.

    • Organizational Affiliation: 
    • Membrane Protein Crystallography Group, Molecular Biosciences Division, Imperial College, London SW7 2AZ, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 363.21 kDa 
  • Atom Count: 25,058 
  • Modeled Residue Count: 3,159 
  • Deposited Residue Count: 3,210 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
A, E, I
588Escherichia coliMutation(s): 0 
EC: 1.3.5.1 (PDB Primary Data), 1.3.99.1 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
Find proteins for P0AC41 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AC41
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AC41
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE IRON-SULFUR SUBUNIT
B, F, J
238Escherichia coliMutation(s): 1 
EC: 1.3.5.1 (PDB Primary Data), 1.3.99.1 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
Find proteins for P07014 (Escherichia coli (strain K12))
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Go to UniProtKB:  P07014
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UniProt GroupP07014
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT
C, G, K
129Escherichia coliMutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for P69054 (Escherichia coli (strain K12))
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UniProt GroupP69054
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT
D, H, L
115Escherichia coliMutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for P0AC44 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AC44
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UniProt GroupP0AC44
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Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD


Download:Ideal Coordinates CCD File
CA [auth I],
M [auth A],
U [auth E]		FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEM

Query on HEM


Download:Ideal Coordinates CCD File
AA [auth G],
IA [auth K],
S [auth C]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SF4

Query on SF4


Download:Ideal Coordinates CCD File
GA [auth J],
Q [auth B],
Y [auth F]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S

Query on F3S


Download:Ideal Coordinates CCD File
HA [auth J],
R [auth B],
Z [auth F]		FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
CBE

Query on CBE


Download:Ideal Coordinates CCD File
BA [auth G],
JA [auth K],
T [auth C]		2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE
C12 H13 N O2 S
GYSSRZJIHXQEHQ-UHFFFAOYSA-N
FES

Query on FES


Download:Ideal Coordinates CCD File
FA [auth J],
P [auth B],
X [auth F]		FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
TEO

Query on TEO


Download:Ideal Coordinates CCD File
DA [auth I],
N [auth A],
V [auth E]		MALATE LIKE INTERMEDIATE
C4 H4 O5
QFBHYOKSQPPXHZ-UWTATZPHSA-L
NA

Query on NA


Download:Ideal Coordinates CCD File
EA [auth I],
O [auth A],
W [auth E]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.222 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.853α = 90
b = 183.803β = 90
c = 202.777γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-01-30
    Changes: Atomic model, Data collection, Database references
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 2.2: 2024-11-13
    Changes: Structure summary