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PDBsum entry 3crc

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
3crc
Jmol
Contents
Protein chains
225 a.a. *
Ligands
ATP
Metals
_MG
Waters ×13
* Residue conservation analysis
PDB id:
3crc
Name: Hydrolase
Title: Crystal structure of escherichia coli mazg, the regulator of nutritional stress response
Structure: Protein mazg. Chain: a, b. Synonym: nucleotide pyrophophohydrolase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k-12. Gene: mazg. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.00Å     R-factor:   0.222     R-free:   0.345
Authors: S.Lee,M.H.Kim,B.S.Kang,J.S.Kim,Y.G.Kim,K.J.Kim
Key ref:
S.Lee et al. (2008). Crystal structure of Escherichia coli MazG, the regulator of nutritional stress response. J Biol Chem, 283, 15232-15240. PubMed id: 18353782 DOI: 10.1074/jbc.M800479200
Date:
05-Apr-08     Release date:   22-Apr-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AEY3  (MAZG_ECOLI) -  Nucleoside triphosphate pyrophosphohydrolase
Seq:
Struc:
263 a.a.
225 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.6.1.8  - Atp diphosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = AMP + diphosphate
ATP
+ H(2)O
= AMP
+ diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M800479200 J Biol Chem 283:15232-15240 (2008)
PubMed id: 18353782  
 
 
Crystal structure of Escherichia coli MazG, the regulator of nutritional stress response.
S.Lee, M.H.Kim, B.S.Kang, J.S.Kim, G.H.Kim, Y.G.Kim, K.J.Kim.
 
  ABSTRACT  
 
MazG is a nucleoside triphosphate pyrophosphohydrolase that hydrolyzes all canonical nucleoside triphosphates. The mazG gene located downstream from the chromosomal mazEF "addiction module," that mediated programmed cell death in Escherichia coli. MazG activity is inhibited by the MazEF complex both in vivo and in vitro. Enzymatic activity of MazG in vivo affects the cellular level of guanosine 3',5'-bispyrophosphate (ppGpp), synthesized by RelA under amino acid starvation. The reduction of ppGpp, caused by MazG, may extend the period of cell survival under nutritional stress. Here we describe the first crystal structure of active MazG from E. coli, which is composed of two similarly folded globular domains in tandem. Among the two putative catalytic domains, only the C-terminal domain has well ordered active sites and exhibits an NTPase activity. The MazG-ATP complex structure and subsequent mutagenesis studies explain the peculiar active site environment accommodating all eight canonical NTPs as substrates. In vivo nutrient starvation experiments show that the C terminus NTPase activity is responsible for the regulation of bacterial cell survival under nutritional stress.
 
  Selected figure(s)  
 
Figure 3.
FIGURE 3. The active site of the EcMazG C-terminal domain. A, diagram showing the ATP molecule and a magnesium ion bound at the active site of the EcMazG CD. The 2F[o] - F[c] electron density (black mesh) is contoured at 1.0 . Carbons, oxygens, nitrogens, and phosphates are shown as green, red, blue, and orange, respectively. B, diagram showing the active site of the EcMazG CD bound with an ATP molecule. Secondary structure elements from two different polypeptides are labeled a and b. The ATP molecule is presented as a ball-and-stick model. Residues involved in the magnesium coordination, enzyme catalysis, and hydrophobic cavity formation for adenine base binding are labeled and presented as a light green stick model. Ionic and hydrogen bonds are shown with red dotted lines. A magnesium ion is presented with as a green ball. C, surface-fill model of EcMazG bound with ATP. ATP molecules bound at the C-terminal active sites are shown with a stick model. Only one ATP molecule was bound at one (right side) of the two C-terminal active sites with no ATP molecule at the other active site (left side), which the side chain of Met^241 from the symmetry-related molecule occupies, and an ATP molecule was modeled in the diagram. D, NTPase activity assays. Hydrolysis of ATP to AMP was carried out using wild type and 14 point mutants of EcMazG. An EcMazG mutant used for each reaction was identified at the top of the TLC. Detailed reaction procedures are described under "Experimental Procedures." E and F, toxic effect of mutant EcMazG on cell growth. E. coli strain BL21 mazG was transformed with plasmids expressing an appropriate protein. The transformants were grown to an A[600] of 0.2, and 1 mM IPTG was added for induction. Cell growth was then measured at A[600]. A[600] at 300 min after the IPTG induction on E was redrawn and differentiated on F.
Figure 6.
FIGURE 6. mazEFG promoters are inhibited under SH-induced starvation conditions. E. coli strain MC4100 mazEFG relA^+ was transformed with the pSK10 6-p[ef] plasmid (24). At A[600] of 0.2, bacterial culture was divided into two flasks, one of which was supplemented with 1 mg/ml SH. At the indicated time points, samples were taken for total RNA isolation and primer extension reaction (see "Experimental Procedures"). C and G, sequence reactions of the same plasmid carried out with the terminators ddCTP and ddGTP, respectively.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 15232-15240) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20024656 C.Lambert, P.Ivanov, and R.E.Sockett (2010).
A transcriptional "Scream" early response of E. coli prey to predatory invasion by Bdellovibrio.
  Curr Microbiol, 60, 419-427.  
20662890 M.B.Sullivan, K.H.Huang, J.C.Ignacio-Espinoza, A.M.Berlin, L.Kelly, P.R.Weigele, A.S.DeFrancesco, S.E.Kern, L.R.Thompson, S.Young, C.Yandava, R.Fu, B.Krastins, M.Chase, D.Sarracino, M.S.Osburne, M.R.Henn, and S.W.Chisholm (2010).
Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments.
  Environ Microbiol, 12, 3035-3056.  
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.