1YUN

Crystal Structure of Nicotinic Acid Mononucleotide Adenylyltransferase from Pseudomonas aeruginosa

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.172 

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Literature

Crystal structure of nicotinic acid mononucleotide adenylyltransferase from Pseudomonas aeruginosa in its Apo and substrate-complexed forms reveals a fully open conformation

Yoon, H.J., Kim, H.L., Mikami, B., Suh, S.W.

(2005) J Mol Biol 351: 258-265

  • DOI: 10.1016/j.jmb.2005.06.001
  • Primary Citation of Related Structures:  
    1YUL, 1YUM, 1YUN

  • PubMed Abstract: 

    • The enzyme nicotinic acid mononucleotide adenylyltransferase (NaMN AT; EC 2.7.7.18) is essential for the synthesis of nicotinamide adenine dinucleotide and is a potential target for antibiotics. It catalyzes the transfer of an AMP moiety from ATP to nicotinic acid mononucleotide to form nicotinic acid adenine dinucleotide ...

    The enzyme nicotinic acid mononucleotide adenylyltransferase (NaMN AT; EC 2.7.7.18) is essential for the synthesis of nicotinamide adenine dinucleotide and is a potential target for antibiotics. It catalyzes the transfer of an AMP moiety from ATP to nicotinic acid mononucleotide to form nicotinic acid adenine dinucleotide. In order to provide missing structural information on the substrate complexes of NaMN AT and to assist structure-based design of specific inhibitors for antibacterial discovery, we have determined the crystal structure of NaMN AT from Pseudomonas aeruginosa in three distinct states, i.e. the NaMN-bound form at 1.7A resolution and ATP-bound form at 2.0A as well as its apo-form at 2.0A. They represent crucial structural information necessary for better understanding of the substrate recognition and the catalytic mechanism. The substrate-unbound and substrate-complexed structures are all in the fully open conformation and there is little conformational change upon binding each of the substrates. Our structures indicate that a conformational change is necessary to bring the two substrates closer together for initiating the catalysis. We suggest that such a conformational change likely occurs only after both substrates are simultaneously bound in the active site.

    Organizational Affiliation: 

    Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, South Korea.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable nicotinate-nucleotide adenylyltransferaseA, B242Pseudomonas aeruginosaMutation(s): 0 
Gene Names: nadD (PA4006)
EC: 2.7.7.18
UniProt
Find proteins for Q9HX21 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HX21 
Go to UniProtKB:  Q9HX21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HX21
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.172 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.189α = 90
b = 65.199β = 90
c = 110.121γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXLrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-08
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance