2H89

Avian Respiratory Complex II with Malonate Bound

PDB DOI: https://doi.org/10.2210/pdb2H89/pdb

Classification: OXIDOREDUCTASE
Organism(s): Gallus gallus
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2006-06-06 Released: 2006-06-20
Deposition Author(s): Huang, L.S., Shen, J.T., Wang, A.C., Berry, E.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.279
R-Value Work: 0.226
R-Value Observed: 0.229

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the

Huang, L.S., Shen, J.T., Wang, A.C., Berry, E.A.

(null) Biochim Biophys Acta 1757: 1073-1083

PubMed: 16935256 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.bbabio.2006.06.015
Primary Citation of Related Structures:
2H88, 2H89

PubMed Abstract:

Mitochondrial Complex II (succinate:ubiquinone oxidoreductase) is purified in a partially inactivated state, which can be activated by removal of tightly bound oxaloacetate (E.B. Kearney, et al., Biochem. Biophys. Res. Commun. 49 1115-1121). We crystallized Complex II in the presence of oxaloacetate or with the endogenous inhibitor bound. The structure showed a ligand essentially identical to the "malate-like intermediate" found in Shewanella Flavocytochrome c crystallized with fumarate (P. Taylor, et al., Nat. Struct. Biol. 6 1108-1112) Crystallization of Complex II in the presence of excess fumarate also gave the malate-like intermediate or a mixture of that and fumarate at the active site. In order to more conveniently monitor the occupation state of the dicarboxylate site, we are developing a library of UV/Vis spectral effects induced by binding different ligands to the site. Treatment with fumarate results in rapid development of the fumarate difference spectrum and then a very slow conversion into a species spectrally similar to the OAA-liganded complex. Complex II is known to be capable of oxidizing malate to the enol form of oxaloacetate (Y.O. Belikova, et al., Biochim. Biophys. Acta 936 1-9). The observations above suggest it may also be capable of interconverting fumarate and malate. It may be useful for understanding the mechanism and regulation of the enzyme to identify the malate-like intermediate and its pathway of formation from oxaloacetate or fumarate.

Related Citations:

3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme.
Huang, L.S., Sun, G., Cobessi, D., Wang, A.C., Shen, J.T., Tung, E.Y., Anderson, V.E., Berry, E.A.
(2006) J Biol Chem 281: 5965

Crystallization of mitochondrial respiratory complex II from chicken heart: a membrane-protein complex diffracting to 2.0 A
Huang, L.S., Borders, T.M., Shen, J.T., Wang, C.J., Berry, E.A.
(2005) Acta Crystallogr D Biol Crystallogr 61: 380

Crystal structure of mitochondrial respiratory membrane protein complex II.
Sun, F., Huo, X., Zhai, Y., Wang, A., Xu, J., Su, D., Bartlam, M., Rao, Z.
(2005) Cell 121: 1043

Organizational Affiliation:

Physical Biosciences Division, Lawrence Berkeley National Lab., MS 64-0121, 1 Cyclotron Road, Berkeley CA 94720, USA.

Macromolecule Content

Total Structure Weight: 127.46 kDa
Atom Count: 9,302
Modelled Residue Count: 1,095
Deposited Residue Count: 1,116
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT	A	621	Gallus gallus	Mutation(s): 0 Gene Names: SDHA EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for Q9YHT1 (Gallus gallus) Explore Q9YHT1 Go to UniProtKB: Q9YHT1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9YHT1
Protein Feature View Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinate dehydrogenase Ip subunit	B	252	Gallus gallus	Mutation(s): 0 Gene Names: SDHB EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for Q9YHT2 (Gallus gallus) Explore Q9YHT2 Go to UniProtKB: Q9YHT2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9YHT2
Protein Feature View Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT	C	140	Gallus gallus	Mutation(s): 0 EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for D0VWW3 (Gallus gallus) Explore D0VWW3 Go to UniProtKB: D0VWW3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VWW3
Protein Feature View Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SUCCINATE DEHYDROGENASE CYTOCHROME B, SMALL SUBUNIT	D	103	Gallus gallus	Mutation(s): 0 Gene Names: SDHD, RCJMB04_23p7 EC: 1.3.5.1 Membrane Entity: Yes
UniProt
Find proteins for Q5ZIS0 (Gallus gallus) Explore Q5ZIS0 Go to UniProtKB: Q5ZIS0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5ZIS0
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Ligand Interaction
PEE Query on PEE Download Ideal Coordinates CCD File SDF format, chain MA [auth C] SDF format, chain WA [auth D] MOL2 format, chain MA [auth C] MOL2 format, chain WA [auth D]	MA [auth C], WA [auth D]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Ligand Interaction
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain LA [auth C] MOL2 format, chain LA [auth C]	LA [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Ligand Interaction
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B]	Y [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-VKOJMFJBAC		Ligand Interaction
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain Z [auth B] MOL2 format, chain Z [auth B]	Z [auth B]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-MZMDZPPWAW		Ligand Interaction
BHG Query on BHG Download Ideal Coordinates CCD File SDF format, chain KA [auth C] MOL2 format, chain KA [auth C]	KA [auth C]	hexyl beta-D-galactopyranoside C₁₂ H₂₄ O₆ JVAZJLFFSJARQM-YBXAARCKSA-N		Ligand Interaction
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain X [auth B] MOL2 format, chain X [auth B]	X [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Ligand Interaction
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Ligand Interaction
K Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain W [auth B] MOL2 format, chain E [auth A] MOL2 format, chain W [auth B]	E [auth A], W [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Ligand Interaction
UNL Query on UNL Download Ideal Coordinates CCD File	AA [auth B] AB [auth D] BA [auth B] BB [auth D] CA [auth B] AA [auth B], AB [auth D], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], EA [auth B], FA [auth B], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], L [auth A], M [auth A], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C], XA [auth D], YA [auth D], ZA [auth D]	Unknown ligand NPYPAHLBTDXSSS-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.279
R-Value Work: 0.226
R-Value Observed: 0.229
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.52	α = 90
b = 84.118	β = 90
c = 292.212	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
Blu-Ice	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-06-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-06-20
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2014-10-29
Changes: Non-polymer description
Version 1.4: 2017-10-18
Changes: Refinement description
Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Database references, Derived calculations, Structure summary
Version 2.0: 2023-08-30
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary