1GX7

Best model of the electron transfer complex between cytochrome c3 and [Fe]-hydrogenase

PDB DOI: https://doi.org/10.2210/pdb1GX7/pdb

Classification: OXIDOREDUCTASE
Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
Mutation(s): No

Deposited: 2002-03-28 Released: 2003-07-31
Deposition Author(s): Elantak, L., Morelli, X., Bornet, O., Hatchikian, C., Czjzek, M., Dolla, A., Guerlesquin, F.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Submitted: 1

Method: THEORETICAL MODEL

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

The Cytochrome C(3)-[Fe]-Hydrogenase Electron-Transfer Complex: Structural Model by NMR Restrained Docking

Elantak, L., Morelli, X., Bornet, O., Hatchikian, C., Czjzek, M., Dolla, A., Guerlesquin, F.

(2003) FEBS Lett 548: 1

PubMed: 12885397 Search on PubMed
DOI: https://doi.org/10.1016/s0014-5793(03)00718-x
Primary Citation of Related Structures:
1GX7

PubMed Abstract:
Cytochrome c(3) (M(r) 13000) is a low redox potential cytochrome specific of the anaerobic metabolism in sulfate-reducing bacteria. This tetrahemic cytochrome is an intermediate between the [Fe]-hydrogenase and the cytochrome Hmc in Desulfovibrio vulgaris Hildenborough strain. The present work describes the structural model of the cytochrome c(3)-[Fe]-hydrogenase complex obtained by nuclear magnetic resonance restrained docking. This model connects the distal cluster of the [Fe]-hydrogenase to heme 4 of the cytochrome, the same heme found in the interaction with cytochrome Hmc. This result gives evidence that cytochrome c(3) is an electron shuttle between the periplasmic hydrogenase and the Hmc membrane-bound complex.

Organizational Affiliation

Unité de Bioénergétique et Ingénierie des Protéines, IBSM-CNRS, 31 chemin Joseph Aiguier, 13402 Cedex 20, Marseille, France. guerlesq@ibsm.cnrs-mrs.fr

Macromolecule Content

Total Structure Weight: 65.87 kDa
Atom Count: 4,541
Modelled Residue Count: 566
Deposited Residue Count: 566
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIPLASMIC [FE] HYDROGENASE LARGE SUBUNIT	A	371	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0 EC: 1.18.99.1
UniProt
Find proteins for P07598 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P07598 Go to UniProtKB: P07598
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07598
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIPLASMIC [FE] HYDROGENASE SMALL SUBUNIT	B [auth D]	88	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0 EC: 1.18.99.1
UniProt
Find proteins for P07603 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P07603 Go to UniProtKB: P07603
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07603
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C3	C [auth E]	107	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0
UniProt
Find proteins for P00131 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P00131 Go to UniProtKB: P00131
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00131
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain Q [auth E] MOL2 format, chain N [auth E] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth E]	N [auth E], O [auth E], P [auth E], Q [auth E]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth E]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
PDT Query on PDT Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	1,3-PROPANEDITHIOL C₃ H₈ S₂ ZJLMKPKYJBQJNH-UHFFFAOYSA-N		Interactions Focus chain G [auth A]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	H [auth A], I [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A]
CMO Query on CMO Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	L [auth A], M [auth A]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A]
CYN Query on CYN Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	J [auth A], K [auth A]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A]