5IGR

Macrolide 2'-phosphotransferase type I - complex with GDP and oleandomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Basis for Kinase-Mediated Macrolide Antibiotic Resistance.

Fong, D.H.Burk, D.L.Blanchet, J.Yan, A.Y.Berghuis, A.M.

(2017) Structure 25: 750-761.e5

  • DOI: 10.1016/j.str.2017.03.007
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The macrolides are a class of antibiotic, characterized by a large macrocyclic lactone ring that can be inactivated by macrolide phosphotransferase enzymes. We present structures for MPH(2')-I and MPH(2')-II in the apo state, and in complex with GTP ...

    The macrolides are a class of antibiotic, characterized by a large macrocyclic lactone ring that can be inactivated by macrolide phosphotransferase enzymes. We present structures for MPH(2')-I and MPH(2')-II in the apo state, and in complex with GTP analogs and six different macrolides. These represent the first structures from the two main classes of macrolide phosphotransferases. The structures show that the enzymes are related to the aminoglycoside phosphotransferases, but are distinguished from them by the presence of a large interdomain linker that contributes to an expanded antibiotic binding pocket. This pocket is largely hydrophobic, with a negatively charged patch located at a conserved aspartate residue, rationalizing the broad-spectrum resistance conferred by the enzymes. Complementary mutation studies provide insights into factors governing substrate specificity. A comparison with macrolides bound to their natural target, the 50S ribosome, suggests avenues for next-generation antibiotic development.


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada; Department of Microbiology & Immunology, McGill University, Montréal, QC H3A 2B4, Canada; Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montréal, QC H3G 0B1, Canada. Electronic address: albert.berghuis@mcgill.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrolide 2'-phosphotransferaseA301Escherichia coliMutation(s): 0 
Gene Names: 
mphAmph(A)mph2A4X18_25005A4X18_26080A6M24_25350ACM48_26150AN669_16770APT94_14590APZ14_31330AZ95_0038ECONIH1_26770ERS085366_04054ERS139269_04809ERS150873_04753ETN48_p0083HMPREF3040_01642orf00017pCTXM123_C0996_11pKC394-009UN86_19875A9R57_28020AKG29_00750AM465_27035AWB10_22655B6V57_21760B6V57_26915B9M99_28110B9N33_26275B9T59_28660BANRA_05393BE963_00520BEN53_26060BFD68_26420BJJ90_27660BK248_28265BK292_28790BK296_27590BK334_26695BK373_25655BK375_28440BK383_16405BON83_00200BON86_00135BON94_01620BON96_04030BvCmsSIP044_05438BVL39_07775BVL39_26555C5P01_27830C5P44_28325C6669_28275C7235_26780CF006_26500CI641_023240CI641_027265CIG45_25125CQP61_00510CR538_26720CRT43_27540CRX46_26190CWS33_26285D0X26_00065D0X26_28390D3O91_28150D3P01_27215D4U49_26725D4U49_28850D4V08_26930D4V08_28620D9K54_18860DB359_27580DBQ99_00755DJ503_27015DL545_01115DL545_26280DM102_27005DM129_26590DM129_28130DM296_25000DM296_26920DMC44_24460DMC44_26180DMZ50_26400DMZ50_28240DS732_30505E2148_26085E2855_05768EA159_24760EA167_25450EA191_26920EA203_25400ECTO124_05299EF082_27695EF082_28360EGT48_01480EHH55_26515EI021_26230EI028_24600EI041_22580EIA21_26660EIZ86_23520EIZ93_26315EJC75_00570ELT20_22120ELT33_25215ELT34_24245ELV08_25535ELV15_24060ELV24_24180ELV24_25785ELV28_26235ELV28_27675ELV28_29590ELX79_23940ELX79_27660ELX83_25990ELX83_26675ELY23_24430ELY23_26140ELY50_24960ELY50_26940EQ823_24855EST51_05890ExPECSC019_03592ExPECSC065_05095EXX13_27015EYD11_23960F1E13_26070F1E19_25850F9059_23040FORC82_p033FQR64_24755FQZ46_09375FTV93_29750GII91_24610HmCmsJML146_04797MS6198_B122MS8345_A00018NCTC13846_04924RCS28_PI0046RCS42_P0046RCS51_P0074RCS55TR727_P0021RCS65_P0021RCS78_P0037RCS79_P0002SAMEA4362930_00091SAMEA4370330_00104SAMEA4370365_00007SAMEA4370473_00005U12A_A00165U14A_A00117YDC107_4986

Find proteins for Q47396 (Escherichia coli)
Explore Q47396 
Go to UniProtKB:  Q47396
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZIO
Query on ZIO

Download CCD File 
A
(3S,5R,6S,7R,8R,11R,12S,13R,14S,15S)-6-HYDROXY-5,7,8,11,13,15-HEXAMETHYL-4,10-DIOXO-14-{[3,4,6-TRIDEOXY-3-(DIMETHYLAMINO)-BETA-D-XYLO-HEXOPYRANOSYL]OXY}-1,9-DIOXASPIRO[2.13]HEXADEC-12-YL 2,6-DIDEOXY-3-O-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSIDE
C35 H61 N O12
RZPAKFUAFGMUPI-KGIGTXTPSA-N
 Ligand Interaction
GDP
Query on GDP

Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
IPA
Query on IPA

Download CCD File 
A
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
NH4
Query on NH4

Download CCD File 
A
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.11α = 90
b = 45.11β = 90
c = 246.8γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-13107

Revision History 

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-05-03
    Changes: Database references
  • Version 1.2: 2017-05-17
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence