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PDBsum entry 4mva

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protein ligands metals Protein-protein interface(s) links
Isomerase PDB id
4mva
Jmol
Contents
Protein chains
255 a.a.
Ligands
UVW ×2
PO4
EDO ×2
PEG
Metals
_CL
Waters ×908
PDB id:
4mva
Name: Isomerase
Title: 1.43 angstrom resolution crystal structure of triosephosphat isomerase (tpia) from escherichia coli in complex with acet phosphate.
Structure: Triosephosphate isomerase. Chain: a, b. Fragment: triosephosphate isomerase (tpia). Synonym: tim, triose-phosphate isomerase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 595496. Strain: k-12 substr. Mg1655. Gene: bwg_3588, tpia. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.43Å     R-factor:   0.136     R-free:   0.156
Authors: G.Minasov,M.L.Kuhn,I.Dubrovska,J.Winsor,L.Shuvalova,S.Grimsh K.Kwon,W.F.Anderson,Center For Structural Genomics Of Infec Diseases (Csgid)
Key ref: M.L.Kuhn et al. (2014). Structural, kinetic and proteomic characterization of acetyl phosphate-dependent bacterial protein acetylation. PLoS One, 9, e94816. PubMed id: 24756028 DOI: 10.1371/journal.pone.0094816
Date:
23-Sep-13     Release date:   16-Apr-14    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
C5A086  (C5A086_ECOBW) -  Triosephosphate isomerase
Seq:
Struc:
255 a.a.
255 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.3.1.1  - Triose-phosphate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glyceraldehyde 3-phosphate = glycerone phosphate
D-glyceraldehyde 3-phosphate
Bound ligand (Het Group name = UVW)
matches with 63.64% similarity
= glycerone phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1371/journal.pone.0094816 PLoS One 9:e94816 (2014)
PubMed id: 24756028  
 
 
Structural, kinetic and proteomic characterization of acetyl phosphate-dependent bacterial protein acetylation.
M.L.Kuhn, B.Zemaitaitis, L.I.Hu, A.Sahu, D.Sorensen, G.Minasov, B.P.Lima, M.Scholle, M.Mrksich, W.F.Anderson, B.W.Gibson, B.Schilling, A.J.Wolfe.
 
  ABSTRACT  
 
The emerging view of Nε-lysine acetylation in eukaryotes is of a relatively abundant post-translational modification (PTM) that has a major impact on the function, structure, stability and/or location of thousands of proteins involved in diverse cellular processes. This PTM is typically considered to arise by the donation of the acetyl group from acetyl-coenzyme A (acCoA) to the ε-amino group of a lysine residue that is reversibly catalyzed by lysine acetyltransferases and deacetylases. Here, we provide genetic, mass spectrometric, biochemical and structural evidence that Nε-lysine acetylation is an equally abundant and important PTM in bacteria. Applying a recently developed, label-free and global mass spectrometric approach to an isogenic set of mutants, we detected acetylation of thousands of lysine residues on hundreds of Escherichia coli proteins that participate in diverse and often essential cellular processes, including translation, transcription and central metabolism. Many of these acetylations were regulated in an acetyl phosphate (acP)-dependent manner, providing compelling evidence for a recently reported mechanism of bacterial Nε-lysine acetylation. These mass spectrometric data, coupled with observations made by crystallography, biochemistry, and additional mass spectrometry showed that this acP-dependent acetylation is both non-enzymatic and specific, with specificity determined by the accessibility, reactivity and three-dimensional microenvironment of the target lysine. Crystallographic evidence shows acP can bind to proteins in active sites and cofactor binding sites, but also potentially anywhere molecules with a phosphate moiety could bind. Finally, we provide evidence that acP-dependent acetylation can impact the function of critical enzymes, including glyceraldehyde-3-phosphate dehydrogenase, triosephosphate isomerase, and RNA polymerase.