7MCB

Crystal structure of Staphylococcus aureus Cystathionine gamma lyase Holoenzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Inhibitors of bacterial H 2 S biogenesis targeting antibiotic resistance and tolerance.

Shatalin, K.Nuthanakanti, A.Kaushik, A.Shishov, D.Peselis, A.Shamovsky, I.Pani, B.Lechpammer, M.Vasilyev, N.Shatalina, E.Rebatchouk, D.Mironov, A.Fedichev, P.Serganov, A.Nudler, E.

(2021) Science 372: 1169-1175

  • DOI: https://doi.org/10.1126/science.abd8377
  • Primary Citation of Related Structures:  
    7MCB, 7MCL, 7MCN, 7MCP, 7MCQ, 7MCT, 7MCU, 7MCY, 7MD0, 7MD1, 7MD6, 7MD8, 7MD9, 7MDA, 7MDB

  • PubMed Abstract: 

    Emergent resistance to all clinical antibiotics calls for the next generation of therapeutics. Here we report an effective antimicrobial strategy targeting the bacterial hydrogen sulfide (H 2 S)-mediated defense system. We identified cystathionine γ-lyase (CSE) as the primary generator of H 2 S in two major human pathogens, Staphylococcus aureus and Pseudomonas aeruginosa , and discovered small molecules that inhibit bacterial CSE. These inhibitors potentiate bactericidal antibiotics against both pathogens in vitro and in mouse models of infection. CSE inhibitors also suppress bacterial tolerance, disrupting biofilm formation and substantially reducing the number of persister bacteria that survive antibiotic treatment. Our results establish bacterial H 2 S as a multifunctional defense factor and CSE as a drug target for versatile antibiotic enhancers.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional cystathionine gamma-lyase/homocysteine desulfhydraseA [auth H]380Staphylococcus aureusMutation(s): 1 
Gene Names: 
mccBmccB_2BTN44_10510DD547_00421DQV53_02590EP54_01605EQ90_13355FA040_13395G0X12_04165G6Y10_12435GO746_10250GO803_10255GO805_07485GO821_10445GO894_05080GO942_04060HMPREF2819_13610HMPREF3211_01439NCTC10654_00533NCTC10702_00840NCTC10988_00626SAMEA1029528_01119SAMEA1029547_02560SAMEA1029553_00881SAMEA103891286_02662SAMEA1964876_02233SAMEA1965205_02550SAMEA1966505_02559SAMEA1969349_02528SAMEA1969845_00024SAMEA1971706_00840SAMEA1972827_00442SAMEA2076212_02307SAMEA2076218_02633SAMEA2076220_02515SAMEA2076226_02545SAMEA2076463_02448SAMEA2076464_02504SAMEA2076470_02202SAMEA2076472_02415SAMEA2076478_01397SAMEA2076480_02228SAMEA2076481_02579SAMEA2076743_02529SAMEA2076745_00024SAMEA2076746_01199SAMEA2076747_02516SAMEA2076749_02428SAMEA2076751_02538SAMEA2076752_00581SAMEA2076755_02246SAMEA2076756_02304SAMEA2076758_02592SAMEA2076759_02587SAMEA2076761_00997SAMEA2076762_02546SAMEA2076763_01275SAMEA2076764_00443SAMEA2076765_02426SAMEA2077023_00443SAMEA2077025_02246SAMEA2077027_02519SAMEA2077029_02492SAMEA2077031_02282SAMEA2077034_02536SAMEA2077035_00908SAMEA2077039_00580SAMEA2077040_02514SAMEA2077041_00442SAMEA2077044_02519SAMEA2077045_01356SAMEA2077046_02211SAMEA2077293_01201SAMEA2077294_01116SAMEA2077295_02535SAMEA2077297_02465SAMEA2077300_00660SAMEA2077301_02506SAMEA2077302_01011SAMEA2077303_02488SAMEA2077307_02470SAMEA2077832_02515SAMEA2078252_01326SAMEA2078256_02526SAMEA2078307_01240SAMEA2078308_02477SAMEA2078553_02466SAMEA2078558_00909SAMEA2078560_01135SAMEA2078569_01369SAMEA2078570_02481SAMEA2078572_01608SAMEA2078824_02504SAMEA2078837_01023SAMEA2079048_02598SAMEA2079051_01218SAMEA2079277_01392SAMEA2079291_02442SAMEA2079503_01420SAMEA2079507_02480SAMEA2079512_02454SAMEA2079517_02461SAMEA2079724_02523SAMEA2079727_02402SAMEA2079728_02358SAMEA2079732_00024SAMEA2079946_02619SAMEA2079949_02348SAMEA2079951_02599SAMEA2079952_00024SAMEA2079957_00024SAMEA2079958_00024SAMEA2079960_02599SAMEA2079961_02614SAMEA2079968_02549SAMEA2080329_00310SAMEA2080330_00310SAMEA2080334_02579SAMEA2080433_00024SAMEA2080812_02589SAMEA2080898_01599SAMEA2080900_02516SAMEA2080904_02530SAMEA2080913_02537SAMEA2081043_02522SAMEA2081053_02264SAMEA2081054_02235SAMEA2081055_02550SAMEA2081060_02563SAMEA2081211_02363SAMEA2081213_02446SAMEA2081218_00838SAMEA2081341_02527SAMEA2081342_02593SAMEA2081349_02540SAMEA2081359_02598SAMEA2081362_00464SAMEA2081468_01079SAMEA2081474_00910SAMEA2081475_02534SAMEA2081476_02404SAMEA2081479_00996SAMEA2081480_00533SAMEA2081560_02486SAMEA2081561_02504SAMEA2081564_01449SAMEA2081567_02515SAMEA2081568_01446SAMEA2081569_02545SAMEA2081570_01449SAMEA2081571_01216SAMEA2081572_02471SAMEA2081573_02217SAMEA2081575_00580SAMEA2081577_01158SAMEA2081578_02511SAMEA2081579_02531SAMEA2081581_02162SAMEA2081582_02344SAMEA2081673_02599SAMEA2081674_02397SAMEA4008573_02705SAMEA4008676_02295SAMEA70146418_02721SAMEA958766_00501SAMEA958770_02469SAMEA958772_00350SAMEA958778_00586SAMEA958779_02116SAMEA958785_02543SAMEA958793_02555SAMEA958798_02471SAMEA958804_02558SAMEA958810_02365SAMEA958836_00976SAMEA958838_01939SAMEA958845_00024SAMEA958846_02565SAMEA958848_02402SAMEA958855_02196SAMEA958858_00594SAMEA958898_01850SAMEA958906_02198SAMEA958924_02531SAMEA958925_02436SAMEA958951_01115SAMEA958953_00350SAMEA958961_02116SAMEA958979_00024SAMEA958987_02419SAMEA958995_02394

EC: 4.4.1.1 (PDB Primary Data), 4.4.1.8 (PDB Primary Data), 2.5.1.48 (PDB Primary Data)
UniProt
Find proteins for X5E0F1 (Staphylococcus aureus)
Explore X5E0F1 
Go to UniProtKB:  X5E0F1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupX5E0F1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
B [auth H]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth H],
F [auth H],
G [auth H],
H
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth H],
D [auth H]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A [auth H]L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.133α = 90
b = 105.133β = 90
c = 288.148γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesPR171734
Department of Defense (DOD, United States)United StatesPR171734P1
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-23
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2023-11-15
    Changes: Data collection