4MVJ

2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3-phosphate Dehydrogenase A (gapA) from Escherichia coli Modified by Acetyl Phosphate.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural, kinetic and proteomic characterization of acetyl phosphate-dependent bacterial protein acetylation.

Kuhn, M.L.Zemaitaitis, B.Hu, L.I.Sahu, A.Sorensen, D.Minasov, G.Lima, B.P.Scholle, M.Mrksich, M.Anderson, W.F.Gibson, B.W.Schilling, B.Wolfe, A.J.

(2014) Plos One 9: e94816-e94816

  • DOI: 10.1371/journal.pone.0094816
  • Primary Citation of Related Structures:  

  • PubMed 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 cell ...

    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.


    Organizational Affiliation

    Center for Structural Genomics of Infectious Diseases, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glyceraldehyde-3-phosphate dehydrogenase A
A, B, C, K, N
355N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glyceraldehyde-3-phosphate dehydrogenase A
D, L
355N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Glyceraldehyde-3-phosphate Dehydrogenase A
E
355N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Glyceraldehyde-3-phosphate Dehydrogenase A
F, J, O
355N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Glyceraldehyde-3-phosphate Dehydrogenase A
G
355N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Glyceraldehyde-3-phosphate Dehydrogenase A
H
355N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Glyceraldehyde-3-phosphate Dehydrogenase A
I
355N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Glyceraldehyde-3-phosphate Dehydrogenase A
M
355N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Glyceraldehyde-3-phosphate Dehydrogenase A
P
355N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, D, E, F, H, I, J, L, P
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
POP
Query on POP

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Download CCD File 
A, B, F, G, J, M
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B, C, D, E, G, H, I, K, M, N
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
H
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAD
Query on NAD

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Download CCD File 
C, D, E, I, K, O, P
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
J
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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H
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
H
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
UVW
Query on UVW

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Download CCD File 
M
ACETYLPHOSPHATE
C2 H5 O5 P
LIPOUNRJVLNBCD-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
A, B, C, E, F, G, H, I, J, K, M, N, O, P
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
SCY
Query on SCY
G, H, P
L-PEPTIDE LINKINGC5 H9 N O3 SCYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 145.879α = 90.00
b = 69.688β = 98.80
c = 271.923γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data scaling
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2014-05-07
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description