5IGI

Macrolide 2'-phosphotransferase type I - complex with guanosine and azithromycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    5IWU, 5IGP, 5IH1, 5IH0, 5IGR, 5IGH, 5IGJ, 5IGI, 5IGT, 5IGS, 5IGV, 5IGU, 5IGW, 5IGZ, 5IGY

  • 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 analogs and six different macrolides ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Macrolide 2'-phosphotransferaseA301Escherichia coliMutation(s): 0 
Gene Names: 
mphAmph(A)mph2AM267_25240AM268_24740AN205_25580AN669_16770ASU34_20250AZ95_0038ECONIH1_26770ERS085366_04054ERS085367_04848ERS139269_04809ERS150873_04753ETN48_p0083orf00017pCTXM123_C0996_11pKC394-009SK74_04859SK86_03516UN86_19875A9R57_28020AKG29_00750AM465_27035APT94_14590APZ14_31330AWB10_22655B6V57_21760B6V57_26915B9M99_28110B9N33_26275B9T59_28660BANRA_05393BE963_00520BEN53_26060BFD68_26420BJJ90_27660BK248_28265BK292_28790BK296_27590BK334_26695BK373_25655BK375_28440BK383_16405BON83_00200BON86_00135BON94_01620BON96_04030BON98_24665BvCmsSIP044_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_24760EA164_24545EA167_25450EA191_26920EA203_25400EA433_24880ECTO124_05299EF082_27695EF082_28360EGT48_01480EHH55_26515EI021_26230EI028_24600EI041_22580EIA21_26660EIZ93_26315EJC75_00570ELT17_24440ELT17_26465ELT20_22120ELT33_25215ELV00_24775ELV08_25535ELV15_24060ELV22_23870ELV22_25960ELV24_24180ELV24_25785ELV28_26235ELV28_27675ELV28_29590ELX56_25505ELX56_25985ELX76_26525ELX76_27685ELX79_23940ELX79_27660ELX83_25990ELX83_26675ELY23_24430ELY23_26140ELY41_23030ELY41_28165ELY50_24960ELY50_26940EQ823_24855EST51_05890ExPECSC019_03592ExPECSC065_05095EXX13_27015EYD11_23960F1E13_26070F1E19_25850F9040_20575F9059_23040FORC82_p033FQR64_24755FQZ46_09375FTV93_29750G3565_27960G5616_24605GII91_24610GP698_23880GZS12_24705HmCmsJML146_04797HMPREF3040_01642MS6198_B122MS8345_A00018NCTC13846_04924RCS105_pI0109RCS28_PI0046RCS42_P0046RCS51_P0074RCS55TR727_P0021RCS57_p0100RCS65_P0021RCS78_P0037RCS79_P0002SAMEA4362930_00091SAMEA4370330_00104SAMEA4370365_00007SAMEA4370473_00005U12A_A00165U14A_A00117YDC107_4986

UniProt
Find proteins for Q47396 (Escherichia coli)
Explore Q47396 
Go to UniProtKB:  Q47396
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZIT (Subject of Investigation/LOI)
Query on ZIT

Download Ideal Coordinates CCD File 
C [auth A]AZITHROMYCIN
C38 H72 N2 O12
MQTOSJVFKKJCRP-BICOPXKESA-N
 Ligand Interaction
GMP (Subject of Investigation/LOI)
Query on GMP

Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE
C10 H13 N5 O5
NYHBQMYGNKIUIF-UUOKFMHZSA-N
 Ligand Interaction
IPA
Query on IPA

Download Ideal Coordinates CCD File 
D [auth A]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ZIT Binding MOAD:  5IGI Kd: 170 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.31α = 90
b = 45.31β = 90
c = 247.42γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • 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