6D9T

BshA from Staphylococcus aureus complexed with UDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A structural and functional analysis of the glycosyltransferase BshA from Staphylococcus aureus: Insights into the reaction mechanism and regulation of bacillithiol production.

Royer, C.J.Cook, P.D.

(2019) Protein Sci 28: 1083-1094

  • DOI: 10.1002/pro.3617
  • Primary Citation of Related Structures:  
    6D9T, 6N1X

  • PubMed Abstract: 
  • Bacillithiol is a glucosamine-derived antioxidant found in several pathogenic Gram-positive bacteria. The compound is involved in maintaining the appropriate redox state within the cell as well as detoxifying foreign agents like the antibiotic fosfomycin ...

    Bacillithiol is a glucosamine-derived antioxidant found in several pathogenic Gram-positive bacteria. The compound is involved in maintaining the appropriate redox state within the cell as well as detoxifying foreign agents like the antibiotic fosfomycin. Bacillithiol is produced via the action of three enzymes, including BshA, a retaining GT-B glycosyltransferase that utilizes UDP-N-acetylglucosamine and l-malate to produce N-acetylglucosaminyl-malate. Recent studies suggest that retaining GT-B glycosyltransferases like BshA utilize a substrate-assisted mechanism that goes through an S N i-like transition state. In a previous study, we relied on X-ray crystallography as well as computational simulations to hypothesize the manner in which substrates would bind the enzyme, but several questions about substrate binding and the role of one of the amino acid residues persisted. Another study demonstrated that BshA might be subject to feedback inhibition by bacillithiol, but this phenomenon was not analyzed further to determine the exact mechanism of inhibition. Here we present X-ray crystallographic structures and steady-state kinetics results that help elucidate both of these issues. Our ligand-bound crystal structures demonstrate that the active site provides an appropriate steric and geometric arrangement of ligands to facilitate the substrate-assisted mechanism. Finally, we show that bacillithiol is competitive for UDP-N-acetylglucosamine with a K i value near 120-130 μM and likely binds within the BshA active site, suggesting that bacillithiol modulates BshA activity via feedback inhibition. The work presented here furthers our understanding of bacillithiol metabolism and can aid in the development of inhibitors to counteract resistance to antibiotics such as fosfomycin.


    Organizational Affiliation

    Department of Chemistry, Grand Valley State University, Allendale, Michigan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycosyl transferaseA400Staphylococcus aureusMutation(s): 0 
Gene Names: 
pimB_2BTN44_05260EP54_02400EQ90_10145ERS365775_02315bshApimBpimB_1DD547_01484DQV53_07850FA040_07610G0V24_03480G0X12_07355G0Z18_04135G6Y10_10895GO746_12320GO803_01480GO805_07220GO821_01520GO894_06050GO942_13355HMPREF2819_13975NCTC10654_01509NCTC10702_02324NCTC10988_01716NCTC9944_01480RK64_07835SAMEA1029528_01502SAMEA1029547_00898SAMEA1029553_00519SAMEA1964876_01470SAMEA1965205_01383SAMEA1966505_01513SAMEA1969349_01455SAMEA1969845_01863SAMEA1971706_00868SAMEA1972827_01651SAMEA2076212_01787SAMEA2076218_01853SAMEA2076220_01939SAMEA2076226_01369SAMEA2076463_01121SAMEA2076464_01120SAMEA2076470_01340SAMEA2076472_01258SAMEA2076478_01462SAMEA2076480_01189SAMEA2076481_01842SAMEA2076743_01399SAMEA2076745_01727SAMEA2076746_01527SAMEA2076747_01132SAMEA2076749_01443SAMEA2076751_01254SAMEA2076752_01203SAMEA2076755_01092SAMEA2076756_01155SAMEA2076758_00994SAMEA2076759_01026SAMEA2076761_01448SAMEA2076762_01336SAMEA2076763_00859SAMEA2076764_01615SAMEA2076765_01633SAMEA2077023_01570SAMEA2077025_00720SAMEA2077027_01345SAMEA2077029_01360SAMEA2077031_01478SAMEA2077034_01401SAMEA2077035_01124SAMEA2077039_01260SAMEA2077040_00928SAMEA2077041_01544SAMEA2077044_01416SAMEA2077045_01491SAMEA2077046_01285SAMEA2077293_01419SAMEA2077294_01524SAMEA2077295_01292SAMEA2077297_01218SAMEA2077300_01522SAMEA2077301_01289SAMEA2077302_01434SAMEA2077303_01299SAMEA2077307_01250SAMEA2077832_01595SAMEA2078252_01543SAMEA2078256_01146SAMEA2078307_01527SAMEA2078308_01117SAMEA2078553_01020SAMEA2078558_01323SAMEA2078560_01422SAMEA2078569_01585SAMEA2078570_01455SAMEA2078572_01673SAMEA2078824_01191SAMEA2078837_01241SAMEA2079048_01336SAMEA2079051_01439SAMEA2079277_01995SAMEA2079291_02320SAMEA2079503_01484SAMEA2079507_01192SAMEA2079512_02288SAMEA2079517_02232SAMEA2079724_01524SAMEA2079727_01799SAMEA2079728_01756SAMEA2079732_01843SAMEA2079742_01871SAMEA2079946_01811SAMEA2079949_01778SAMEA2079951_01368SAMEA2079952_01607SAMEA2079957_01725SAMEA2079958_01635SAMEA2079960_02022SAMEA2079961_01796SAMEA2079968_01527SAMEA2080329_01655SAMEA2080330_01725SAMEA2080334_01745SAMEA2080433_01927SAMEA2080812_01057SAMEA2080898_01824SAMEA2080900_01448SAMEA2080904_01306SAMEA2080913_01266SAMEA2081043_01522SAMEA2081053_01429SAMEA2081054_01077SAMEA2081055_01415SAMEA2081060_01636SAMEA2081211_00670SAMEA2081213_02281SAMEA2081218_01462SAMEA2081341_01528SAMEA2081342_01799SAMEA2081349_01677SAMEA2081359_01432SAMEA2081362_01810SAMEA2081468_01214SAMEA2081474_01319SAMEA2081475_01465SAMEA2081476_00775SAMEA2081479_01287SAMEA2081480_01497SAMEA2081560_01171SAMEA2081561_01393SAMEA2081564_01584SAMEA2081567_01573SAMEA2081568_01581SAMEA2081569_01130SAMEA2081570_01584SAMEA2081571_01509SAMEA2081572_01250SAMEA2081573_01159SAMEA2081575_01477SAMEA2081577_01416SAMEA2081578_01099SAMEA2081579_01378SAMEA2081581_01283SAMEA2081582_01589SAMEA2081673_01643SAMEA2081674_01880SAMEA958766_01335SAMEA958770_02667SAMEA958772_01555SAMEA958778_02403SAMEA958779_02319SAMEA958785_02418SAMEA958793_02708SAMEA958798_01441SAMEA958804_01617SAMEA958810_01195SAMEA958836_01427SAMEA958838_01695SAMEA958845_02399SAMEA958846_01931SAMEA958848_01618SAMEA958855_01481SAMEA958858_01320SAMEA958870_00218SAMEA958898_01114SAMEA958906_01318SAMEA958924_01465SAMEA958925_01489SAMEA958951_01483SAMEA958953_02642SAMEA958961_00308SAMEA958979_02483SAMEA958987_02217SAMEA958995_00968

EC: 2.4.1.57 (PDB Primary Data), 2.4.1.345 (UniProt), 2.4.1 (UniProt)
UniProt
Find proteins for A0A068A5A2 (Staphylococcus aureus)
Explore A0A068A5A2 
Go to UniProtKB:  A0A068A5A2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDP (Subject of Investigation/LOI)
Query on UDP

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.38α = 90
b = 135.38β = 90
c = 135.38γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R15GM117488

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence