3CSX

Structural characterization of a protein in the DUF683 family- crystal structure of cce_0567 from the cyanobacterium Cyanothece 51142.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.220 

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Literature

Structural characterization of the protein cce_0567 from Cyanothece 51142, a metalloprotein associated with nitrogen fixation in the DUF683 family.

Buchko, G.W.Robinson, H.Addlagatta, A.

(2009) Biochim Biophys Acta 1794: 627-633

  • DOI: 10.1016/j.bbapap.2009.01.002
  • Primary Citation of Related Structures:  
    3CSX

  • PubMed Abstract: 
  • The genomes of many cyanobacteria contain the sequence for a small protein with a common "Domain of Unknown Function" grouped into the DUF683 protein family. While the biological function of DUF683 is still not known, their genomic location within nitrogen fixation clusters suggests that DUF683 proteins may play a role in the process ...

    The genomes of many cyanobacteria contain the sequence for a small protein with a common "Domain of Unknown Function" grouped into the DUF683 protein family. While the biological function of DUF683 is still not known, their genomic location within nitrogen fixation clusters suggests that DUF683 proteins may play a role in the process. The diurnal cyanobacterium Cyanothece sp. PCC 51142 contains a gene for a protein that falls into the DUF683 family, cce_0567 (78 aa, 9.0 kDa). In an effort to elucidate the biochemical role DUF683 proteins may play in nitrogen fixation, we have determined the first crystal structure for a protein in this family, cce_0567, to 1.84 A resolution. Cce_0567 crystallized in space group P2(1) with two protein molecules and one Ni(2+) cation per asymmetric unit. The protein is composed of two alpha-helices, residues P11 to G41 (alpha1) and L49-E74 (alpha2), with the second alpha-helix containing a short 3(10)-helix (Y46-N48). A four-residue linker (L42-D45) between the helices allows them to form an anti-parallel bundle and cross over each other towards their termini. In solution it is likely that two molecules of cce_0567 form a rod-like dimer by the stacking interactions of approximately 1/2 of the protein. Histidine-36 is highly conserved in all known DUF683 proteins and the N2 nitrogen of the H36 side chain of each molecule in the dimer is coordinated with Ni(2+) in the crystal structure. The divalent cation Ni(2+) was titrated into (15)N-labeled cce_0567 and chemical shift perturbations were observed only in the (1)H-(15)N HSQC spectra for residues at, or near, the site of Ni(2+) binding observed in the crystal structure. There was no evidence for an increase in the size of cce_0567 upon binding Ni(2+), even in large molar excess of Ni(2+), indicating that a metal was not required for dimer formation. Circular dichroism spectroscopy indicated that cce_0567 was extremely robust, with a melting temperature of approximately 62 degrees C that was reversible.


    Organizational Affiliation

    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA. garry.buchko@pnl.gov



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized proteinA, B81CyanotheceMutation(s): 0 
UniProt
Find proteins for A1KYE3 (Crocosphaera subtropica (strain ATCC 51142 / BH68))
Explore A1KYE3 
Go to UniProtKB:  A1KYE3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1KYE3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download Ideal Coordinates CCD File 
C [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.436α = 90
b = 38.381β = 96.7
c = 62.643γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance