6EAC | pdb_00006eac

Pseudomonas syringae SelO

  • Classification: TRANSFERASE
  • Organism(s): Pseudomonas syringae
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-08-02 Released: 2018-10-03 
  • Deposition Author(s): Tomchick, D.R., Tagliabracci, V.S., Sreelatha, A.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Robert A. Welch Foundation, Other government

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 
    0.212 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history. 

Literature

Protein AMPylation by an Evolutionarily Conserved Pseudokinase.

Sreelatha, A., Yee, S.S., Lopez, V.A., Park, B.C., Kinch, L.N., Pilch, S., Servage, K.A., Zhang, J., Jiou, J., Karasiewicz-Urbanska, M., Lobocka, M., Grishin, N.V., Orth, K., Kucharczyk, R., Pawlowski, K., Tomchick, D.R., Tagliabracci, V.S.

(2018) Cell 175: 809

  • DOI: https://doi.org/10.1016/j.cell.2018.08.046
  • Primary Citation Related Structures: 
    6EAC

  • PubMed Abstract: 

    Approximately 10% of human protein kinases are believed to be inactive and named pseudokinases because they lack residues required for catalysis. Here, we show that the highly conserved pseudokinase selenoprotein-O (SelO) transfers AMP from ATP to Ser, Thr, and Tyr residues on protein substrates (AMPylation), uncovering a previously unrecognized activity for a member of the protein kinase superfamily. The crystal structure of a SelO homolog reveals a protein kinase-like fold with ATP flipped in the active site, thus providing a structural basis for catalysis. SelO pseudokinases localize to the mitochondria and AMPylate proteins involved in redox homeostasis. Consequently, SelO activity is necessary for the proper cellular response to oxidative stress. Our results suggest that AMPylation may be a more widespread post-translational modification than previously appreciated and that pseudokinases should be analyzed for alternative transferase activities.

    • Organizational Affiliation: 
    • Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

Macromolecule Content 

  • Total Structure Weight: 226.33 kDa 
  • Atom Count: 16,098 
  • Modeled Residue Count: 1,902 
  • Deposited Residue Count: 1,952 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SelO
A, B, C, D
488Pseudomonas syringaeMutation(s): 0 
EC: 2.7.7 (PDB Primary Data), 2.7.7.108 (UniProt)
UniProt
Find proteins for Q87VB1 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000))
Explore Q87VB1 
Go to UniProtKB:  Q87VB1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ87VB1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP

Query on ANP


Download:Ideal Coordinates CCD File
CB [auth D],
DA [auth B],
J [auth A],
RA [auth C]		PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
PEG

Query on PEG


Download:Ideal Coordinates CCD File
HB [auth D],
KA [auth B],
U [auth A],
UA [auth C],
VA [auth C]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
DB [auth D]
EA [auth B]
EB [auth D]
FA [auth B]
FB [auth D]
DB [auth D],
EA [auth B],
EB [auth D],
FA [auth B],
FB [auth D],
GA [auth B],
GB [auth D],
HA [auth B],
IA [auth B],
JA [auth B],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
SA [auth C],
T [auth A],
TA [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT


Download:Ideal Coordinates CCD File
LA [auth B],
V [auth A],
W [auth A],
WA [auth C]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA

Query on CA


Download:Ideal Coordinates CCD File
AA [auth B]
AB [auth D]
BA [auth B]
F [auth A]
G [auth A]
AA [auth B],
AB [auth D],
BA [auth B],
F [auth A],
G [auth A],
H [auth A],
K [auth A],
NA [auth C],
OA [auth C],
PA [auth C],
Y [auth B],
YA [auth D],
Z [auth B],
ZA [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
BB [auth D],
CA [auth B],
I [auth A],
QA [auth C]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG


Download:Ideal Coordinates CCD File
E [auth A],
MA [auth C],
X [auth B],
XA [auth D]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free:  0.212 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.174α = 90
b = 158.056β = 90
c = 227.248γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXmodel building
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR00DK099254
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM094575
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM115188
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesT32DK007257-37
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM008203-29
Robert A. Welch FoundationUnited StatesI-1911
Robert A. Welch FoundationUnited StatesI-1505
Robert A. Welch FoundationUnited StatesI-1561
Other governmentUnited StatesRP170674

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2018-10-17
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.5: 2020-03-04
    Changes: Data collection
  • Version 1.6: 2024-03-13
    Changes: Data collection, Database references, Derived calculations