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PDBsum entry 1kqp

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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
1kqp
Jmol
Contents
Protein chains
271 a.a. *
Ligands
EDO ×10
ADJ ×2
POP ×2
Metals
_MG ×5
Waters ×714
* Residue conservation analysis
PDB id:
1kqp
Name: Ligase
Title: Nh3-dependent NAD+ synthetase from bacillus subtilis at 1 a
Structure: Nh(3)-dependent NAD(+) synthetase. Chain: a, b. Synonym: nh3-dependent NAD+ synthetase. NAD+ synthase. Spor protein outb. Spore outgrowth factor b. General stress pro gsp38. Engineered: yes. Other_details: complexed with a reaction intermediate NAD-a adj
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: outb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.03Å     R-factor:   0.118     R-free:   0.147
Authors: J.Symersky,Y.Devedjiev,K.Moore,C.Brouillette,L.Delucas
Key ref:
J.Symersky et al. (2002). NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution. Acta Crystallogr D Biol Crystallogr, 58, 1138-1146. PubMed id: 12077433 DOI: 10.1107/S0907444902006698
Date:
07-Jan-02     Release date:   28-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P08164  (NADE_BACSU) -  NH(3)-dependent NAD(+) synthetase
Seq:
Struc:
272 a.a.
271 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.3.1.5  - NAD(+) synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + deamido-NAD+ + NH3 = AMP + diphosphate + NAD+
ATP
+
deamido-NAD(+)
Bound ligand (Het Group name = ADJ)
matches with 66.67% similarity
+ NH(3)
= AMP
+
diphosphate
Bound ligand (Het Group name = POP)
corresponds exactly
+ NAD(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     sporulation resulting in formation of a cellular spore   2 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444902006698 Acta Crystallogr D Biol Crystallogr 58:1138-1146 (2002)
PubMed id: 12077433  
 
 
NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution.
J.Symersky, Y.Devedjiev, K.Moore, C.Brouillette, L.DeLucas.
 
  ABSTRACT  
 
The final step of NAD+ biosynthesis includes an amide transfer to nicotinic acid adenine dinucleotide (NaAD) catalyzed by NAD+ synthetase. This enzyme was co-crystallized in microgravity with natural substrates NaAD and ATP at pH 8.5. The crystal was exposed to ammonium ions, synchrotron diffraction data were collected and the atomic model was refined anisotropically at 1 A resolution to R = 11.63%. Both binding sites are occupied by the NAD-adenylate intermediate, pyrophosphate and two magnesium ions. The atomic resolution of the structure allows better definition of non-planar peptide groups, reveals a low mean anisotropy of protein and substrate atoms and indicates the H-atom positions of the phosphoester group of the reaction intermediate. The phosphoester group is protonated at the carbonyl O atom O7N, suggesting a carbenium-ion structure stabilized by interactions with two solvent sites presumably occupied by ammonia and a water molecule. A mechanism is proposed for the second catalytic step, which includes a nucleophilic attack by the ammonia molecule on the intermediate.
 
  Selected figure(s)  
 
Figure 5.
Figure 5 Spatial relationship between the intermediate protonated at O7N and cation-binding sites M+(I) and M+(II). Distances are shown in for subunit A. C atoms are in green, N atoms in blue, O atoms in red, P atoms in magenta and H atoms in cyan. Hydrophobic residues are all in gray, magnesium ions in black and the monovalent cation-binding sites M+(I) and M+(II) are shown as golden spheres. Rendered using RIBBONS (Carson, 1997[Carson, M. (1997). Methods Enzymol. 277, 493-505.]).
Figure 6.
Figure 6 (a) Stabilization of the protonated intermediate by the hydrogen bond with ammonia positioned in the cation-binding site M+(I) and a hypothetical hydrogen bond with water molecule in the cation-binding site M+(II) releasing the ammonia molecule for nucleophilic attack. (b) Reaction scheme for the second catalytic step of NAD^+ synthetase. The NAD-adenylate intermediate reacts with ammonia to form NAD^+ and AMP and two protons are released. R[1] represents the ADP-nicotinosyl moiety and R[2] represents the AMP moiety.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 1138-1146) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20300652 D.E.Almonacid, E.R.Yera, J.B.Mitchell, and P.C.Babbitt (2010).
Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.
  PLoS Comput Biol, 6, e1000700.  
19554628 J.A.Mobley, and A.Poliakov (2009).
Detection of early unfolding events in a dimeric protein by amide proton exchange and native electrospray mass spectrometry.
  Protein Sci, 18, 1620-1627.  
19270703 N.LaRonde-LeBlanc, M.Resto, and B.Gerratana (2009).
Regulation of active site coupling in glutamine-dependent NAD(+) synthetase.
  Nat Struct Mol Biol, 16, 421-429.
PDB code: 3dla
19249205 W.B.Moro, Z.Yang, T.A.Kane, C.G.Brouillette, and W.J.Brouillette (2009).
Virtual screening to identify lead inhibitors for bacterial NAD synthetase (NADs).
  Bioorg Med Chem Lett, 19, 2001-2005.  
15699042 R.Jauch, A.Humm, R.Huber, and M.C.Wahl (2005).
Structures of Escherichia coli NAD synthetase with substrates and products reveal mechanistic rearrangements.
  J Biol Chem, 280, 15131-15140.
PDB codes: 1wxe 1wxf 1wxg 1wxh 1wxi
14978314 Z.W.Yang, S.W.Tendian, W.M.Carson, W.J.Brouillette, L.J.Delucas, and C.G.Brouillette (2004).
Dimethyl sulfoxide at 2.5% (v/v) alters the structural cooperativity and unfolding mechanism of dimeric bacterial NAD+ synthetase.
  Protein Sci, 13, 830-841.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.