1KAM

Structure of Bacillus subtilis Nicotinic Acid Mononucleotide Adenylyl Transferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Identification, characterization, and crystal structure of Bacillus subtilis nicotinic acid mononucleotide adenylyltransferase.

Olland, A.M.Underwood, K.W.Czerwinski, R.M.Lo, M.C.Aulabaugh, A.Bard, J.Stahl, M.L.Somers, W.S.Sullivan, F.X.Chopra, R.

(2002) J Biol Chem 277: 3698-3707

  • DOI: 10.1074/jbc.M109670200
  • Primary Citation of Related Structures:  
    1KAM, 1KAQ

  • PubMed Abstract: 
  • The nadD gene, encoding the enzyme nicotinic acid mononucleotide (NaMN) adenylyltransferase (AT), is essential for the synthesis of NAD and subsequent viability of the cell. The nadD gene in Bacillus subtilis (yqeJ) was identified by sequence homolog ...

    The nadD gene, encoding the enzyme nicotinic acid mononucleotide (NaMN) adenylyltransferase (AT), is essential for the synthesis of NAD and subsequent viability of the cell. The nadD gene in Bacillus subtilis (yqeJ) was identified by sequence homology with other bacterial nadD genes and by biochemical characterization of the gene product. NaMN AT catalyzes the reversible adenylation of both NaMN and the nicotinamide mononucleotide (NMN) but shows specificity for the nicotinate. In contrast to other known NMN ATs, biophysical characterizations reveal it to be a dimer. The NaMN AT crystal structure was determined for both the apo enzyme and product-bound form, to 2.1 and 3.2 A, respectively. The structures reveal a "functional" dimer conserved in both crystal forms and a monomer fold common to members of the nucleotidyl-transferase alpha/beta phosphodiesterase superfamily. A structural comparison with family members suggests a new conserved motif (SXXXX(R/K)) at the N terminus of an alpha-helix, which is not part of the shared fold. Interactions of the nicotinic acid with backbone atoms indicate the structural basis for specificity.


    Organizational Affiliation

    Wyeth-Ayerst Research, Department of Biological Chemistry, Cambridge, Massachusetts 02140, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASEABCD194Bacillus subtilisMutation(s): 0 
Gene Names: nadD
EC: 2.7.7.18
Find proteins for P54455 (Bacillus subtilis (strain 168))
Explore P54455 
Go to UniProtKB:  P54455
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.977α = 90
b = 126.103β = 92.73
c = 70.579γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-07-12
    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: 2014-11-12
    Changes: Structure summary