Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.60 kDa 
• Atom Count: 664 
• Residue Count: 71 
• Unique protein chains: 1

2LDO

Solution structure of triheme cytochrome PpcA from Geobacter sulfurreducens reveals the structural origin of the redox-Bohr effect

• DOI: 10.2210/pdb2LDO/pdb
• BMRB: 16842

• Classification: ELECTRON TRANSPORT
• Organism(s): Geobacter sulfurreducens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-30 Released: 2011-09-07 
• Deposition Author(s): Morgado, L., Paixao, V.B., Bruix, M., Salgueiro, C.A.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Revealing the structural origin of the redox-Bohr effect: the first solution structure of a cytochrome from Geobacter sulfurreducens.

Morgado, L., Paixao, V.B., Schiffer, M., Pokkuluri, P.R., Bruix, M., Salgueiro, C.A.

(2012) Biochem J 441: 179-187

• PubMed: 21861844 
• DOI: 10.1042/BJ20111103
• Primary Citation of Related Structures:  
  2LDO


• PubMed Abstract: 
  

Gs (Geobacter sulfurreducens) can transfer electrons to the exterior of its cells, a property that makes it a preferential candidate for the development of biotechnological applications. Its genome encodes over 100 cytochromes and, despite their abundance and key functional roles, to date there is no structural information for these proteins in solution. The trihaem cytochrome PpcA might have a crucial role in the conversion of electronic energy into protonmotive force, a fundamental step for ATP synthesis in the presence of extracellular electron acceptors. In the present study, 15N-labelled PpcA was produced and NMR spectroscopy was used to determine its solution structure in the fully reduced state, its backbone dynamics and the pH-dependent conformational changes. The structure obtained is well defined, with an average pairwise rmsd (root mean square deviation) of 0.25 Å (1 Å=0.1 nm) for the backbone atoms and 0.99 Å for all heavy atoms, and constitutes the first solution structure of a Gs cytochrome. The redox-Bohr centre responsible for controlling the electron/proton transfer was identified, as well as the putative interacting regions between PpcA and its redox partners. The solution structure of PpcA will constitute the foundation for studies aimed at mapping out in detail these interacting regions.

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Organizational Affiliation: 

Requimte-CQFB, Department of Chemistry, Faculty of Sciences and Technology, New University of Lisbon, Campus Caparica, 2829-516 Caparica, Portugal.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c3	A	71	Geobacter sulfurreducens	Mutation(s): 0  Gene Names: GSU0612, ppcA, RW64_12645, YM18_0596
Find proteins for Q8GGK7 (Geobacter sulfurreducens) Explore Q8GGK7  Go to UniProtKB:  Q8GGK7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	A	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2LDO Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-30 
• Released Date: 2011-09-07 
Deposition Author(s): Morgado, L., Paixao, V.B., Bruix, M., Salgueiro, C.A.

Revision History 

• Version 1.0: 2011-09-07
  Type: Initial release
  
• Version 1.1: 2011-12-28
  Changes: Database references