7MCB | pdb_00007mcb

Crystal structure of Staphylococcus aureus Cystathionine gamma lyase Holoenzyme

PDB DOI: https://doi.org/10.2210/pdb7MCB/pdb

Classification: LYASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-04-01 Released: 2021-06-23
Deposition Author(s): Nuthanakanti, A., Serganov, A., Kaushik, A.
Funding Organization(s): Department of Defense (DOD, United States), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.184 (Depositor), 0.180 (DCC)
R-Value Work:
0.162 (Depositor), 0.160 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
View more details

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

PubMed: 34112687 Search on PubMedSearch on PubMed Central
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 ₂S)-mediated defense system. We identified cystathionine γ-lyase (CSE) as the primary generator of H ₂S 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 ₂S 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.

Macromolecule Content

Total Structure Weight: 42.17 kDa
Atom Count: 3,216
Modeled Residue Count: 380
Deposited Residue Count: 380
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase	A [auth H]	380	Staphylococcus aureus	Mutation(s): 1 Gene Names: mccB, mccB_2, BTN44_10510, DD547_00421, DQV53_02590, EP54_01605, EQ90_13355, FA040_13395, G0X12_04165, G6Y10_12435... mccB, mccB_2, BTN44_10510, DD547_00421, DQV53_02590, EP54_01605, EQ90_13355, FA040_13395, G0X12_04165, G6Y10_12435, GO746_10250, GO803_10255, GO805_07485, GO821_10445, GO894_05080, GO942_04060, HMPREF2819_13610, HMPREF3211_01439, NCTC10654_00533, NCTC10702_00840, NCTC10988_00626, SAMEA1029528_01119, SAMEA1029547_02560, SAMEA1029553_00881, SAMEA103891286_02662, SAMEA1964876_02233, SAMEA1965205_02550, SAMEA1966505_02559, SAMEA1969349_02528, SAMEA1969845_00024, SAMEA1971706_00840, SAMEA1972827_00442, SAMEA2076212_02307, SAMEA2076218_02633, SAMEA2076220_02515, SAMEA2076226_02545, SAMEA2076463_02448, SAMEA2076464_02504, SAMEA2076470_02202, SAMEA2076472_02415, SAMEA2076478_01397, SAMEA2076480_02228, SAMEA2076481_02579, SAMEA2076743_02529, SAMEA2076745_00024, SAMEA2076746_01199, SAMEA2076747_02516, SAMEA2076749_02428, SAMEA2076751_02538, SAMEA2076752_00581, SAMEA2076755_02246, SAMEA2076756_02304, SAMEA2076758_02592, SAMEA2076759_02587, SAMEA2076761_00997, SAMEA2076762_02546, SAMEA2076763_01275, SAMEA2076764_00443, SAMEA2076765_02426, SAMEA2077023_00443, SAMEA2077025_02246, SAMEA2077027_02519, SAMEA2077029_02492, SAMEA2077031_02282, SAMEA2077034_02536, SAMEA2077035_00908, SAMEA2077039_00580, SAMEA2077040_02514, SAMEA2077041_00442, SAMEA2077044_02519, SAMEA2077045_01356, SAMEA2077046_02211, SAMEA2077293_01201, SAMEA2077294_01116, SAMEA2077295_02535, SAMEA2077297_02465, SAMEA2077300_00660, SAMEA2077301_02506, SAMEA2077302_01011, SAMEA2077303_02488, SAMEA2077307_02470, SAMEA2077832_02515, SAMEA2078252_01326, SAMEA2078256_02526, SAMEA2078307_01240, SAMEA2078308_02477, SAMEA2078553_02466, SAMEA2078558_00909, SAMEA2078560_01135, SAMEA2078569_01369, SAMEA2078570_02481, SAMEA2078572_01608, SAMEA2078824_02504, SAMEA2078837_01023, SAMEA2079048_02598, SAMEA2079051_01218, SAMEA2079277_01392, SAMEA2079291_02442, SAMEA2079503_01420, SAMEA2079507_02480, SAMEA2079512_02454, SAMEA2079517_02461, SAMEA2079724_02523, SAMEA2079727_02402, SAMEA2079728_02358, SAMEA2079732_00024, SAMEA2079946_02619, SAMEA2079949_02348, SAMEA2079951_02599, SAMEA2079952_00024, SAMEA2079957_00024, SAMEA2079958_00024, SAMEA2079960_02599, SAMEA2079961_02614, SAMEA2079968_02549, SAMEA2080329_00310, SAMEA2080330_00310, SAMEA2080334_02579, SAMEA2080433_00024, SAMEA2080812_02589, SAMEA2080898_01599, SAMEA2080900_02516, SAMEA2080904_02530, SAMEA2080913_02537, SAMEA2081043_02522, SAMEA2081053_02264, SAMEA2081054_02235, SAMEA2081055_02550, SAMEA2081060_02563, SAMEA2081211_02363, SAMEA2081213_02446, SAMEA2081218_00838, SAMEA2081341_02527, SAMEA2081342_02593, SAMEA2081349_02540, SAMEA2081359_02598, SAMEA2081362_00464, SAMEA2081468_01079, SAMEA2081474_00910, SAMEA2081475_02534, SAMEA2081476_02404, SAMEA2081479_00996, SAMEA2081480_00533, SAMEA2081560_02486, SAMEA2081561_02504, SAMEA2081564_01449, SAMEA2081567_02515, SAMEA2081568_01446, SAMEA2081569_02545, SAMEA2081570_01449, SAMEA2081571_01216, SAMEA2081572_02471, SAMEA2081573_02217, SAMEA2081575_00580, SAMEA2081577_01158, SAMEA2081578_02511, SAMEA2081579_02531, SAMEA2081581_02162, SAMEA2081582_02344, SAMEA2081673_02599, SAMEA2081674_02397, SAMEA4008573_02705, SAMEA4008676_02295, SAMEA70146418_02721, SAMEA958766_00501, SAMEA958770_02469, SAMEA958772_00350, SAMEA958778_00586, SAMEA958779_02116, SAMEA958785_02543, SAMEA958793_02555, SAMEA958798_02471, SAMEA958804_02558, SAMEA958810_02365, SAMEA958836_00976, SAMEA958838_01939, SAMEA958845_00024, SAMEA958846_02565, SAMEA958848_02402, SAMEA958855_02196, SAMEA958858_00594, SAMEA958898_01850, SAMEA958906_02198, SAMEA958924_02531, SAMEA958925_02436, SAMEA958951_01115, SAMEA958953_00350, SAMEA958961_02116, SAMEA958979_00024, SAMEA958987_02419, SAMEA958995_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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	X5E0F1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain B [auth H] MOL2 format, chain B [auth H] mmCIF format, chain B [auth H]	B [auth H]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain B [auth H] Interactions & Density Focus chain B [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain F [auth H] SDF format, chain G [auth H] SDF format, chain H MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] MOL2 format, chain H mmCIF format, chain E [auth H] mmCIF format, chain F [auth H] mmCIF format, chain G [auth H] mmCIF format, chain H	E [auth H], F [auth H], G [auth H], H	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Interactions & Density Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth H] SDF format, chain D [auth H] MOL2 format, chain C [auth H] MOL2 format, chain D [auth H] mmCIF format, chain C [auth H] mmCIF format, chain D [auth H]	C [auth H], D [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth H] Focus chain D [auth H] Interactions & Density Focus chain C [auth H] Focus chain D [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A [auth H]	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.184 (Depositor), 0.180 (DCC)
R-Value Work: 0.162 (Depositor), 0.160 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.133	α = 90
b = 105.133	β = 90
c = 288.148	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-06-23

Deposition Author(s):

Nuthanakanti, A.

Serganov, A.

Kaushik, A.

Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	PR171734
Department of Defense (DOD, United States)	United States	PR171734P1
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