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PDBsum entry 1ee1
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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
1ee1

 

 

 

 

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Contents
Protein chains
271 a.a. *
246 a.a. *
Ligands
DND ×2
ATP
Metals
_MG
Waters ×397
* Residue conservation analysis
PDB id:
1ee1
Name: Ligase
Title: Crystal structure of nh3-dependent NAD+ synthetase from bacillus subtilis complexed with one molecule atp, two molecules deamido-NAD+ and one mg2+ ion
Structure: Nh(3)-dependent NAD(+) synthetase. Chain: a, b. Synonym: NAD(+) synthetase. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: nade. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.06Å     R-factor:   0.154     R-free:   0.219
Authors: Y.Devedjiev,J.Symersky,R.Singh,M.Jedrzejas,C.Brouillette, W.Brouillette,D.Muccio,D.Chattopadhyay,L.Delucas
Key ref:
Y.Devedjiev et al. (2001). Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis. Acta Crystallogr D Biol Crystallogr, 57, 806-812. PubMed id: 11375500 DOI: 10.1107/S0907444901003523
Date:
28-Jan-00     Release date:   06-Jun-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P08164  (NADE_BACSU) -  NH(3)-dependent NAD(+) synthetase from Bacillus subtilis (strain 168)
Seq:
Struc: 		272 a.a.
271 a.a.
Protein chain
P08164  (NADE_BACSU) -  NH(3)-dependent NAD(+) synthetase from Bacillus subtilis (strain 168)
Seq:
Struc: 		272 a.a.
246 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.6.3.1.5  - NAD(+) synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: deamido-NAD+ + NH4+ + ATP = AMP + diphosphate + NAD+ + H+
deamido-NAD(+)
Bound ligand (Het Group name = ATP)
corresponds exactly 		+ NH4(+)
 + ATP
 = AMP
 + diphosphate
 + NAD(+)
 + H(+)
Bound ligand (Het Group name = DND)
matches with 95.56% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1107/S0907444901003523 Acta Crystallogr D Biol Crystallogr 57:806-812 (2001)
PubMed id: 11375500  
 
 
Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis.
Y.Devedjiev, J.Symersky, R.Singh, M.Jedrzejas, C.Brouillette, W.Brouillette, D.Muccio, D.Chattopadhyay, L.DeLucas.
 
  ABSTRACT  
 
The NH(3)-dependent NAD(+) synthetase (NADS) participates in the biosynthesis of nicotinamide adenine dinucleotide (NAD(+)) by transforming nicotinic acid adenine dinucleotide (NaAD) to NAD(+). The structural behavior of the active site, including stabilization of flexible loops 82-87 and 204-225, has been studied by determination of the crystal structures of complexes of NADS with natural substrates and a substrate analog. Both loops are stabilized independently of NaAD and solely from the ATP-binding site. Analysis of the binding contacts suggests that the minor loop 82-87 is stabilized primarily by a hydrogen bond with the adenine base of ATP. Formation of a coordination complex with Mg(2+) in the ATP-binding site may contribute to the stabilization of the major loop 204-225. The major loop has a role in substrate recognition and stabilization, in addition to the protection of the reaction intermediate described previously. A second and novel Mg(2+) position has been observed closer to the NaAD-binding site in the structure crystallized at pH 7.5, where the enzyme is active. This could therefore be the catalytically active Mg(2+).
 
  Selected figure(s)  
 
Figure 1.
Figure 1 A scheme of the reaction catalyzed by NAD^+ synthetase. 		Figure 6.
Figure 6 Coordination of Mg2+ in the ATP-binding site of NAD^+ synthetase. The nicotinosyl moiety of NaAD is shown in violet, AMP in gold and PP[i] in red; Mg2+ with coordinated O atoms are shown in silver, relevant amino-acid residues are in green and the loop 204-225 is indicated by thin brown lines. Positions Mg(I), Mg(II) and Mg(III) are explained in the text. Coordination of the new Mg(III) position is indicated by thin silver lines. The new conformation of Glu162 at pH 7.5 is shown in cyan. ATP and AMP-CPP are not shown for clarity. Prepared with RIBBONS (Carson, 1997[Carson, M. (1997). Methods Enzymol. 277, 493-505.]).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 806-812) copyright 2001.  
  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
15645437 G.B.Kang, Y.S.Kim, Y.J.Im, S.H.Rho, J.H.Lee, and S.H.Eom (2005).
Crystal structure of NH3-dependent NAD+ synthetase from Helicobacter pylori.
  Proteins, 58, 985-988.
PDB codes: 1xng 1xnh
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.  
12684518 M.Goto, R.Omi, I.Miyahara, M.Sugahara, and K.Hirotsu (2003).
Structures of argininosuccinate synthetase in enzyme-ATP substrates and enzyme-AMP product forms: stereochemistry of the catalytic reaction.
  J Biol Chem, 278, 22964-22971.
PDB codes: 1j1z 1j20 1j21 1kh3
12681931 S.Sutherland (2003).
New antibiotics for anthrax?
  Drug Discov Today, 8, 335-336.  
11844799 M.Goto, Y.Nakajima, and K.Hirotsu (2002).
Crystal structure of argininosuccinate synthetase from Thermus thermophilus HB8. Structural basis for the catalytic action.
  J Biol Chem, 277, 15890-15896.
PDB codes: 1kh1 1kh2 1kor
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.

 

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