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The Open Protein Structure Annotation Network
PDB Keyword
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2fna

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus. Proteins 74 1041-1049 2009
    Site JCSG
    PDB Id 2fna Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1426,13814777, PF01637
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.41 Rfactor 0.174
    Waters
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    Solvent Content 48.53

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 2fna
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
     
    2. Wheel of life, wheel of death: a mechanistic insight into signaling by STAND proteins
    O Danot, E Marquenet, D Vidal-Ingigliardi, E Richet - Structure, 2009 - Elsevier
     
    3. Identification of DNA-binding proteins using structural, electrostatic and evolutionary features
    G Nimrod, A Szilgyi, C Leslie, N Ben-Tal - Journal of molecular biology, 2009 - Elsevier
     
    4. Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus
    Q Xu, CL Rife, D Carlton, MD Miller - Proteins: Structure, , 2009 - Wiley Online Library
     
    5. Multiple structure alignment with msTALI
    P Shealy, H Valafar - BMC bioinformatics, 2012 - biomedcentral.com
     

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    Protein Summary

    The structure of Sulfolobus solfataricus SSO1545 protein (NP_342973) represents a first experimentally determined structure from a large (~200 members) PFAM family (PF01637) of archeal ATPases. Function of proteins from this family is unknown. In numerous genomes, members from this family form two domain proteins with archeal form of Holliday junction resolvase. Predicted functional associations (STRING) are with putative ATPases (Q97YB3_SULSO) and putative DNA-binding proteins (Q97ZV8_SULSO).
     
    Pre-SCOP classifies 2fna N-terminal domain (1-283) in the alpha/beta class, P-loop containing nucleotide triphosphate hydrolase superfamily, extended AAA-ATPase domain family; and the C-terminal domain (284-356) in the all alpha class, winged-helix DNA binding domain superfamily, helicase DNA binding domain family. A DALI structural similarity search returns as top hit the Walker-type ATPase 2qen (Z=35), followed by ORC2 1w5t (Z=19), the apoptosis regulator CED9 2a5y (Z=17) and the cell division control regulator-6 2qby (Z=15). 2fna structure shows strong structural similarity to eukaryotic cell division control proteins and to the NBARC domain in human apoptosis regulating factor (APAF-1) (RMSD of ~3A with sequence identity of ~10%). This similarity extends beyond the core ATP binding Rossman fold domain into the regulatory helical domains.

    HHpred shows a highly significant hit to Walker-type ATPases, eg. 2qen. Comparing the structures 2qen and 2fna (39% sequence identity for 301 aligned residues computed with TopMatch) shows a perfect agreement between the two ADP molecules. Furthermore HHpred reveals a good hit to an ATP-dependent metalloprotease, 1ixz (Z=10), which has a Hg metal ion from MAD phasing bound [Ref]. A similar structure, 1iy1 (Z=10), has the ADP molecule bound and comparing all three structures shows that the ADP and the metal ion are as close as 3A. However, the latter structures are proteases and lack a DNA/RNA binding domain.

    Ligand Summary



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