4OA5

X-ray crystal structure of an O-methyltransferase from Anaplasma phagocytophilum bound to SAH solved by iodide SAD phasing


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

An O-Methyltransferase Is Required for Infection of Tick Cells by Anaplasma phagocytophilum.

Oliva Chavez, A.S.Fairman, J.W.Felsheim, R.F.Nelson, C.M.Herron, M.J.Higgins, L.Burkhardt, N.Y.Oliver, J.D.Markowski, T.W.Kurtti, T.J.Edwards, T.E.Munderloh, U.G.

(2015) PLoS Pathog 11: e1005248-e1005248

  • DOI: https://doi.org/10.1371/journal.ppat.1005248
  • Primary Citation of Related Structures:  
    4OA5, 4OA8, 4PCA, 4PCL

  • PubMed Abstract: 

    Anaplasma phagocytophilum, the causative agent of Human Granulocytic Anaplasmosis (HGA), is an obligately intracellular α-proteobacterium that is transmitted by Ixodes spp ticks. However, the pathogen is not transovarially transmitted between tick generations and therefore needs to survive in both a mammalian host and the arthropod vector to complete its life cycle. To adapt to different environments, pathogens rely on differential gene expression as well as the modification of proteins and other molecules. Random transposon mutagenesis of A. phagocytophilum resulted in an insertion within the coding region of an o-methyltransferase (omt) family 3 gene. In wild-type bacteria, expression of omt was up-regulated during binding to tick cells (ISE6) at 2 hr post-inoculation, but nearly absent by 4 hr p.i. Gene disruption reduced bacterial binding to ISE6 cells, and the mutant bacteria that were able to enter the cells were arrested in their replication and development. Analyses of the proteomes of wild-type versus mutant bacteria during binding to ISE6 cells identified Major Surface Protein 4 (Msp4), but also hypothetical protein APH_0406, as the most differentially methylated. Importantly, two glutamic acid residues (the targets of the OMT) were methyl-modified in wild-type Msp4, whereas a single asparagine (not a target of the OMT) was methylated in APH_0406. In vitro methylation assays demonstrated that recombinant OMT specifically methylated Msp4. Towards a greater understanding of the overall structure and catalytic activity of the OMT, we solved the apo (PDB_ID:4OA8), the S-adenosine homocystein-bound (PDB_ID:4OA5), the SAH-Mn2+ bound (PDB_ID:4PCA), and SAM- Mn2+ bound (PDB_ID:4PCL) X-ray crystal structures of the enzyme. Here, we characterized a mutation in A. phagocytophilum that affected the ability of the bacteria to productively infect cells from its natural vector. Nevertheless, due to the lack of complementation, we cannot rule out secondary mutations.


  • Organizational Affiliation

    Department of Entomology, University of Minnesota, Saint Paul, Minnesota, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O-methyltransferase family protein
A, B, C, D, E
A, B, C, D, E, F
227Anaplasma phagocytophilum str. HZMutation(s): 0 
Gene Names: APH_0584
EC: 2.1.1
UniProt
Find proteins for Q2GKC7 (Anaplasma phagocytophilum (strain HZ))
Explore Q2GKC7 
Go to UniProtKB:  Q2GKC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2GKC7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
CA [auth B]
G [auth A]
HD [auth F]
NC [auth E]
PB [auth D]
CA [auth B],
G [auth A],
HD [auth F],
NC [auth E],
PB [auth D],
UA [auth C]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
AB [auth C]
AC [auth D]
AD [auth E]
AE [auth F]
BB [auth C]
AB [auth C],
AC [auth D],
AD [auth E],
AE [auth F],
BB [auth C],
BC [auth D],
BD [auth E],
BE [auth F],
CB [auth C],
CC [auth D],
CD [auth E],
CE [auth F],
DA [auth B],
DB [auth C],
DC [auth D],
DD [auth E],
DE [auth F],
EA [auth B],
EB [auth C],
EC [auth D],
FA [auth B],
FB [auth C],
FC [auth D],
GA [auth B],
GB [auth C],
GC [auth D],
H [auth A],
HA [auth B],
HB [auth C],
HC [auth D],
I [auth A],
IA [auth B],
IB [auth C],
IC [auth D],
ID [auth F],
J [auth A],
JA [auth B],
JB [auth C],
JC [auth D],
JD [auth F],
K [auth A],
KA [auth B],
KB [auth C],
KC [auth D],
KD [auth F],
L [auth A],
LA [auth B],
LB [auth C],
LD [auth F],
M [auth A],
MA [auth B],
MB [auth C],
MD [auth F],
N [auth A],
NA [auth B],
NB [auth C],
ND [auth F],
O [auth A],
OA [auth B],
OB [auth C],
OC [auth E],
OD [auth F],
P [auth A],
PA [auth B],
PC [auth E],
PD [auth F],
Q [auth A],
QA [auth B],
QB [auth D],
QC [auth E],
QD [auth F],
R [auth A],
RA [auth B],
RB [auth D],
RC [auth E],
RD [auth F],
S [auth A],
SA [auth B],
SB [auth D],
SC [auth E],
SD [auth F],
T [auth A],
TB [auth D],
TC [auth E],
TD [auth F],
U [auth A],
UB [auth D],
UC [auth E],
UD [auth F],
V [auth A],
VA [auth C],
VB [auth D],
VC [auth E],
VD [auth F],
W [auth A],
WA [auth C],
WB [auth D],
WC [auth E],
WD [auth F],
X [auth A],
XA [auth C],
XB [auth D],
XC [auth E],
XD [auth F],
Y [auth A],
YA [auth C],
YB [auth D],
YC [auth E],
YD [auth F],
Z [auth A],
ZA [auth C],
ZB [auth D],
ZC [auth E],
ZD [auth F]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL
Query on GOL

Download Ideal Coordinates CCD File 
GD [auth E],
JE [auth F],
LC [auth D],
MC [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
ED [auth E]
EE [auth F]
FD [auth E]
AA [auth A],
BA [auth A],
ED [auth E],
EE [auth F],
FD [auth E],
FE [auth F],
GE [auth F],
HE [auth F],
IE [auth F],
TA [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 192.36α = 90
b = 72.27β = 124.94
c = 130.84γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2016-01-20
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Refinement description