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 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 


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:  
    4K6A, 4MVA, 4MVJ

  • 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 cellular processes ...

    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

    Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase AA, B, C, K, N355Escherichia coli DH1Mutation(s): 0 
Gene Names: ECDH1ME8569_1723EcDH1_1863gapA
EC: 1.2.1.12
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase AD, L355Escherichia coli DH1Mutation(s): 0 
Gene Names: ECDH1ME8569_1723EcDH1_1863gapA
EC: 1.2.1.12
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate Dehydrogenase AE355Escherichia coli DH1Mutation(s): 0 
Gene Names: ECDH1ME8569_1723EcDH1_1863gapA
EC: 1.2.1.12
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate Dehydrogenase AF, J, O355Escherichia coli DH1Mutation(s): 0 
Gene Names: ECDH1ME8569_1723EcDH1_1863gapA
EC: 1.2.1.12
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate Dehydrogenase AG355Escherichia coli DH1Mutation(s): 0 
Gene Names: ECDH1ME8569_1723EcDH1_1863gapA
EC: 1.2.1.12
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate Dehydrogenase AH355Escherichia coli DH1Mutation(s): 0 
Gene Names: ECDH1ME8569_1723EcDH1_1863gapA
EC: 1.2.1.12
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate Dehydrogenase AI355Escherichia coli DH1Mutation(s): 0 
Gene Names: ECDH1ME8569_1723EcDH1_1863gapA
EC: 1.2.1.12
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate Dehydrogenase AM355Escherichia coli DH1Mutation(s): 0 
Gene Names: ECDH1ME8569_1723EcDH1_1863gapA
EC: 1.2.1.12
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate Dehydrogenase AP355Escherichia coli DH1Mutation(s): 0 
Gene Names: ECDH1ME8569_1723EcDH1_1863gapA
EC: 1.2.1.12
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Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
BD [auth P],
HC [auth K],
JA [auth C],
QA [auth D],
WB [auth I],
BD [auth P],
HC [auth K],
JA [auth C],
QA [auth D],
WB [auth I],
YC [auth O],
ZA [auth E]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
PG4
Query on PG4

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FC [auth J]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
POP
Query on POP

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GC [auth J],
IA [auth B],
JB [auth F],
PB [auth G],
VC [auth M],
GC [auth J],
IA [auth B],
JB [auth F],
PB [auth G],
VC [auth M],
Y [auth A]
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
PGE
Query on PGE

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UB [auth H]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
UVW
Query on UVW

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UC [auth M]ACETYLPHOSPHATE
C2 H5 O5 P
LIPOUNRJVLNBCD-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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VB [auth H]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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AC [auth I],
DC [auth J],
EC [auth J],
ED [auth P],
FD [auth P],
AC [auth I],
DC [auth J],
EC [auth J],
ED [auth P],
FD [auth P],
GB [auth E],
HA [auth B],
IB [auth F],
QC [auth L],
SB [auth H],
V [auth A],
W [auth A],
X [auth A],
XA [auth D],
YA [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ACT
Query on ACT

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TB [auth H]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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AD [auth O],
BA [auth B],
BB [auth E],
BC [auth J],
CA [auth B],
AD [auth O],
BA [auth B],
BB [auth E],
BC [auth J],
CA [auth B],
CB [auth E],
CC [auth J],
CD [auth P],
DA [auth B],
DB [auth E],
DD [auth P],
EA [auth B],
EB [auth E],
FA [auth B],
FB [auth E],
GA [auth B],
HB [auth F],
JC [auth K],
KC [auth K],
LA [auth C],
LB [auth G],
LC [auth K],
MA [auth C],
MB [auth G],
MC [auth K],
NA [auth C],
NB [auth G],
NC [auth K],
OA [auth C],
OB [auth G],
OC [auth K],
PA [auth C],
PC [auth L],
R [auth A],
RB [auth H],
S [auth A],
SA [auth D],
SC [auth M],
T [auth A],
TA [auth D],
TC [auth M],
U [auth A],
UA [auth D],
VA [auth D],
WA [auth D],
XC [auth N],
YB [auth I],
ZB [auth I],
ZC [auth O]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

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AA [auth B],
AB [auth E],
IC [auth K],
KA [auth C],
KB [auth G],
AA [auth B],
AB [auth E],
IC [auth K],
KA [auth C],
KB [auth G],
Q [auth A],
QB [auth H],
RA [auth D],
RC [auth M],
WC [auth N],
XB [auth I],
Z [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
A, B, C, K, N L-PEPTIDE LINKINGC8 H16 N2 O3LYS
SCY
Query on SCY
G L-PEPTIDE LINKINGC5 H9 N O3 SCYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.879α = 90
b = 69.688β = 98.8
c = 271.923γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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