3OUQ

Structure of N-terminal hexaheme fragment of GSU1996


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of a novel dodecaheme cytochrome c from Geobacter sulfurreducens reveals an extended 12nm protein with interacting hemes.

Pokkuluri, P.R.Londer, Y.Y.Duke, N.E.Pessanha, M.Yang, X.Orshonsky, V.Orshonsky, L.Erickson, J.Zagyanskiy, Y.Salgueiro, C.A.Schiffer, M.

(2011) J.Struct.Biol. 174: 223-233

  • DOI: 10.1016/j.jsb.2010.11.022
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Multiheme cytochromes c are important in electron transfer pathways in reduction of both soluble and insoluble Fe(III) by Geobacter sulfurreducens. We determined the crystal structure at 3.2Å resolution of the first dodecaheme cytochrome c (GSU1996) ...

    Multiheme cytochromes c are important in electron transfer pathways in reduction of both soluble and insoluble Fe(III) by Geobacter sulfurreducens. We determined the crystal structure at 3.2Å resolution of the first dodecaheme cytochrome c (GSU1996) along with its N-terminal and C-terminal hexaheme fragments at 2.6 and 2.15Å resolution, respectively. The macroscopic reduction potentials of the full-length protein and its fragments were measured. The sequence of GSU1996 can be divided into four c(7)-type domains (A, B, C and D) with homology to triheme cytochromes c(7). In cytochromes c(7) all three hemes are bis-His coordinated, whereas in c(7)-type domains the last heme is His-Met coordinated. The full-length GSU1996 has a 12nm long crescent shaped structure with the 12 hemes arranged along a polypeptide to form a "nanowire" of hemes; it has a modular structure. Surprisingly, while the C-terminal half of the protein consists of two separate c(7)-type domains (C and D) connected by a small linker, the N-terminal half of the protein has two c(7)-type domains (A and B) that form one structural unit. This is also observed in the AB fragment. There is an unexpected interaction between the hemes at the interface of domains A and B, which form a heme-pair with nearly parallel stacking of their porphyrin rings. The hemes adjacent to each other throughout the protein are within van der Waals distance which enables efficient electron exchange between them. For the first time, the structural details of c(7)-type domains from one multiheme protein were compared.


    Related Citations: 
    • Structure of a novel c7-type three-heme cytochrome domain from a multidomain cytochrome c polymer.
      Pokkuluri, P.R.,Londer, Y.Y.,Duke, N.E.,Erickson, J.,Pessanha, M.,Salgueiro, C.A.,Schiffer, M.
      (2004) Protein Sci. 13: 1684


    Organizational Affiliation

    Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA. rajp@anl.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c family protein
A
161Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)Mutation(s): 0 
Find proteins for Q74BP5 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
Go to UniProtKB:  Q74BP5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.244 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 63.000α = 90.00
b = 84.200β = 90.00
c = 100.900γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance