8GTH

Crystal strucuture of cyt c551 from anoxygenic phototrophic bacterium Roseiflexus castenholzii

PDB DOI: https://doi.org/10.2210/pdb8GTH/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Roseiflexus castenholzii DSM 13941
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-09-08 Released: 2023-09-13
Deposition Author(s): Min, Z.Z., Meng, H.L., Xu, X.L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.272
R-Value Work: 0.242

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

A cytochrome c 551 mediates the cyclic electron transport chain of the anoxygenic phototrophic bacterium Roseiflexus castenholzii.

Yu, L., Min, Z., Liu, M., Xin, Y., Liu, A., Kuang, J., Wu, W., Wu, J., He, H., Xin, J., Blankenship, R.E., Tian, C., Xu, X.

(2024) Plant Commun 5: 100715-100715

PubMed: 37710959 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.xplc.2023.100715
Primary Citation of Related Structures:
8GTH

PubMed Abstract:
Roseiflexus castenholzii is a gram-negative filamentous phototrophic bacterium that carries out anoxygenic photosynthesis through a cyclic electron transport chain (ETC). The ETC is composed of a reaction center (RC)-light-harvesting (LH) complex (rcRC-LH); an alternative complex III (rcACIII), which functionally replaces the cytochrome bc ₁/b ₆f complex; and the periplasmic electron acceptor auracyanin (rcAc). Although compositionally and structurally different from the bc ₁/b ₆f complex, rcACIII plays similar essential roles in oxidizing menaquinol and transferring electrons to the rcAc. However, rcACIII-mediated electron transfer (which includes both an intraprotein route and a downstream route) has not been clearly elucidated, nor have the details of cyclic ETC. Here, we identify a previously unknown monoheme cytochrome c (cyt c ₅₅₁) as a novel periplasmic electron acceptor of rcACIII. It reduces the light-excited rcRC-LH to complete a cyclic ETC. We also reveal the molecular mechanisms involved in the ETC using electron paramagnetic resonance (EPR), spectroelectrochemistry, and enzymatic and structural analyses. We find that electrons released from rcACIII-oxidized menaquinol are transferred to two alternative periplasmic electron acceptors (rcAc and cyt c ₅₅₁), which eventually reduce the rcRC to form the complete cyclic ETC. This work serves as a foundation for further studies of ACIII-mediated electron transfer in anoxygenic photosynthesis and broadens our understanding of the diversity and molecular evolution of prokaryotic ETCs.

Organizational Affiliation

High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.

Macromolecule Content

Total Structure Weight: 77.32 kDa
Atom Count: 4,815
Modelled Residue Count: 617
Deposited Residue Count: 684
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c class I	A B C D [auth E] E [auth F] A, B, C, D [auth E], E [auth F], F [auth D]	114	Roseiflexus castenholzii DSM 13941	Mutation(s): 0 Gene Names: Rcas_2631
UniProt
Find proteins for A7NME2 (Roseiflexus castenholzii (strain DSM 13941 / HLO8)) Explore A7NME2 Go to UniProtKB: A7NME2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7NME2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC (Subject of Investigation/LOI) Query on HEC Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth E] SDF format, chain K [auth F] SDF format, chain L [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth E] MOL2 format, chain K [auth F] MOL2 format, chain L [auth D]	G [auth A] H [auth B] I [auth C] J [auth E] K [auth F] G [auth A], H [auth B], I [auth C], J [auth E], K [auth F], L [auth D]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth E] Focus chain K [auth F] Focus chain L [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth E] Focus chain K [auth F] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.272
R-Value Work: 0.242
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.63	α = 90
b = 71.63	β = 90
c = 349.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
Coot	model building
xia2	data reduction
xia2	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-09-13

Deposition Author(s):

Min, Z.Z.

Meng, H.L.

Xu, X.L.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171227
National Natural Science Foundation of China (NSFC)	China	31870740
National Natural Science Foundation of China (NSFC)	China	31570738