1EXC

CRYSTAL STRUCTURE OF B. SUBTILIS MAF PROTEIN COMPLEXED WITH D-(UTP)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.197 

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This is version 1.3 of the entry. See complete history. 


Literature

Functional implications from crystal structures of the conserved Bacillus subtilis protein Maf with and without dUTP.

Minasov, G., Teplova, M., Stewart, G.C., Koonin, E.V., Anderson, W.F., Egli, M.

(2000) Proc Natl Acad Sci U S A 97: 6328-6333

  • DOI: 10.1073/pnas.97.12.6328
  • Primary Citation of Related Structures:  
    1EX2, 1EXC

  • PubMed Abstract: 

    • Three-dimensional structures of functionally uncharacterized proteins may furnish insight into their functions. The potential benefits of three-dimensional structural information regarding such proteins are particularly obvious when the corresponding genes are conserved during evolution, implying an important function, and no functional classification can be inferred from their sequences ...

    Three-dimensional structures of functionally uncharacterized proteins may furnish insight into their functions. The potential benefits of three-dimensional structural information regarding such proteins are particularly obvious when the corresponding genes are conserved during evolution, implying an important function, and no functional classification can be inferred from their sequences. The Bacillus subtilis Maf protein is representative of a family of proteins that has homologs in many of the completely sequenced genomes from archaea, prokaryotes, and eukaryotes, but whose function is unknown. As an aid in exploring function, we determined the crystal structure of this protein at a resolution of 1.85 A. The structure, in combination with multiple sequence alignment, reveals a putative active site. Phosphate ions present at this site and structural similarities between a portion of Maf and the anticodon-binding domains of several tRNA synthetases suggest that Maf may be a nucleic acid-binding protein. The crystal structure of a Maf-nucleoside triphosphate complex provides support for this hypothesis and hints at di- or oligonucleotides with either 5'- or 3'-terminal phosphate groups as ligands or substrates of Maf. A further clue comes from the observation that the structure of the Maf monomer bears similarity to that of the recently reported Methanococcus jannaschii Mj0226 protein. Just as for Maf, the structure of this predicted NTPase was determined as part of a structural genomics pilot project. The structural relation between Maf and Mj0226 was not apparent from sequence analysis approaches. These results emphasize the potential of structural genomics to reveal new unexpected connections between protein families previously considered unrelated.

    Organizational Affiliation: 

    Department of Molecular Pharmacology and Biological Chemistry and The Drug Discovery Program, Northwestern University Medical School, Chicago, IL 60611, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN MAFA, B189Bacillus subtilisMutation(s): 0 
EC: 3.6.1.9
UniProt
Find proteins for Q02169 (Bacillus subtilis (strain 168))
Explore Q02169 
Go to UniProtKB:  Q02169
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02169
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DUT
Query on DUT
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth B],
G [auth B]		DEOXYURIDINE-5'-TRIPHOSPHATE
C9 H15 N2 O14 P3
AHCYMLUZIRLXAA-SHYZEUOFSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.1α = 90
b = 86.58β = 90
c = 93.73γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection