2FDO

Crystal Structure of the Conserved Protein of Unknown Function AF2331 from Archaeoglobus fulgidus DSM 4304 Reveals a New Type of Alpha/Beta Fold


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of alpha + beta fold.

Wang, S.Kirillova, O.Chruszcz, M.Gront, D.Zimmerman, M.D.Cymborowski, M.T.Shumilin, I.A.Skarina, T.Gorodichtchenskaia, E.Savchenko, A.Edwards, A.M.Minor, W.

(2009) Protein Sci. 18: 2410-2419

  • DOI: 10.1002/pro.251

  • PubMed Abstract: 
  • The structure of AF2331, a 11-kDa orphan protein of unknown function from Archaeoglobus fulgidus, was solved by Se-Met MAD to 2.4 A resolution. The structure consists of an alpha + beta fold formed by an unusual homodimer, where the two core beta-she ...

    The structure of AF2331, a 11-kDa orphan protein of unknown function from Archaeoglobus fulgidus, was solved by Se-Met MAD to 2.4 A resolution. The structure consists of an alpha + beta fold formed by an unusual homodimer, where the two core beta-sheets are interdigitated, containing strands alternating from both subunits. The decrease in solvent-accessible surface area upon dimerization is unusually large (3960 A(2)) for a protein of its size. The percentage of the total surface area buried in the interface (41.1%) is one of the largest observed in a nonredundant set of homodimers in the PDB and is above the mean for nearly all other types of homo-oligomers. AF2331 has no sequence homologs, and no structure similar to AF2331 could be found in the PDB using the CE, TM-align, DALI, or SSM packages. The protein has been identified in Pfam 23.0 as the archetype of a new superfamily and is topologically dissimilar to all other proteins with the "3-Layer (BBA) Sandwich" fold in CATH. Therefore, we propose that AF2331 forms a novel alpha + beta fold. AF2331 contains multiple negatively charged surface clusters and is located on the same operon as the basic protein AF2330. We hypothesize that AF2331 and AF2330 may form a charge-stabilized complex in vivo, though the role of the negatively charged surface clusters is not clear.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein AF2331
B, A
94Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)Mutation(s): 0 
Find proteins for O27953 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Go to UniProtKB:  O27953
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 45.205α = 90.00
b = 48.873β = 90.00
c = 86.693γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MLPHAREphasing
SHELXEmodel building
Omodel building
SOLVEphasing
CCP4phasing
REFMACrefinement
RESOLVEphasing
DMphasing
HKL-2000data scaling
SHELXDphasing
Cootmodel building
SBC-Collectdata collection
HKL-3000phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2006-01-31
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance