6USA | pdb_00006usa

Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and GSK1-bound form

PDB DOI: https://doi.org/10.2210/pdb6USA/pdb

Classification: LYASE/Lyase Inhibitor
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-10-25 Released: 2020-09-30
Deposition Author(s): Chang, C., Michalska, K., Maltseva, N.I., Jedrzejczak, R., McCarren, P., Nag, P.P., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): Global Health Innovative Technology Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.192 (Depositor), 0.191 (DCC)
R-Value Work:
0.158 (Depositor), 0.158 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Allosteric inhibitors of Mycobacterium tuberculosis tryptophan synthase.

Michalska, K., Chang, C., Maltseva, N.I., Jedrzejczak, R., Robertson, G.T., Gusovsky, F., McCarren, P., Schreiber, S.L., Nag, P.P., Joachimiak, A.

(2020) Protein Sci 29: 779-788

PubMed: 31930594 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.3825
Primary Citation Related Structures:
6U6C, 6USA

PubMed Abstract:
Global dispersion of multidrug resistant bacteria is very common and evolution of antibiotic-resistance is occurring at an alarming rate, presenting a formidable challenge for humanity. The development of new therapeuthics with novel molecular targets is urgently needed. Current drugs primarily affect protein, nucleic acid, and cell wall synthesis. Metabolic pathways, including those involved in amino acid biosynthesis, have recently sparked interest in the drug discovery community as potential reservoirs of such novel targets. Tryptophan biosynthesis, utilized by bacteria but absent in humans, represents one of the currently studied processes with a therapeutic focus. It has been shown that tryptophan synthase (TrpAB) is required for survival of Mycobacterium tuberculosis in macrophages and for evading host defense, and therefore is a promising drug target. Here we present crystal structures of TrpAB with two allosteric inhibitors of M. tuberculosis tryptophan synthase that belong to sulfolane and indole-5-sulfonamide chemical scaffolds. We compare our results with previously reported structural and biochemical studies of another, azetidine-containing M. tuberculosis tryptophan synthase inhibitor. This work shows how structurally distinct ligands can occupy the same allosteric site and make specific interactions. It also highlights the potential benefit of targeting more variable allosteric sites of important metabolic enzymes.

Organizational Affiliation

Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois.

Macromolecule Content

Total Structure Weight: 293.53 kDa
Atom Count: 21,114
Modeled Residue Count: 2,602
Deposited Residue Count: 2,744
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase alpha chain	A, C, E, G	276	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: trpA, Rv1613, MTCY01B2.05 EC: 4.2.1.20
UniProt
Find proteins for P9WFY1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFY1 Go to UniProtKB: P9WFY1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WFY1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase beta chain	B, D, F, H	410	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: trpB, Rv1612, MTCY01B2.04 EC: 4.2.1.20
UniProt
Find proteins for P9WFX9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFX9 Go to UniProtKB: P9WFX9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WFX9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PZJ (Subject of Investigation/LOI) Query on PZJ Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain MB [auth H] SDF format, chain QA [auth F] SDF format, chain Y [auth D] MOL2 format, chain L [auth B] MOL2 format, chain MB [auth H] MOL2 format, chain QA [auth F] MOL2 format, chain Y [auth D] mmCIF format, chain L [auth B] mmCIF format, chain MB [auth H] mmCIF format, chain QA [auth F] mmCIF format, chain Y [auth D]	L [auth B], MB [auth H], QA [auth F], Y [auth D]	(3R,4R)-4-[4-(2-Chlorophenyl)piperazin-1-yl]-1,1-dioxothiolan-3-ol C₁₄ H₁₉ Cl N₂ O₃ S CRYVRLLTCKZRFB-KBPBESRZSA-N		Interactions Focus chain L [auth B] Focus chain MB [auth H] Focus chain QA [auth F] Focus chain Y [auth D] Interactions & Density Focus chain L [auth B] Focus chain MB [auth H] Focus chain QA [auth F] Focus chain Y [auth D]
P1T Query on P1T Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain NB [auth H] SDF format, chain RA [auth F] SDF format, chain Z [auth D] MOL2 format, chain M [auth B] MOL2 format, chain NB [auth H] MOL2 format, chain RA [auth F] MOL2 format, chain Z [auth D] mmCIF format, chain M [auth B] mmCIF format, chain NB [auth H] mmCIF format, chain RA [auth F] mmCIF format, chain Z [auth D]	M [auth B], NB [auth H], RA [auth F], Z [auth D]	2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID C₁₁ H₁₅ N₂ O₇ P BXUDKFHCAMQSRX-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain NB [auth H] Focus chain RA [auth F] Focus chain Z [auth D] Interactions & Density Focus chain M [auth B] Focus chain NB [auth H] Focus chain RA [auth F] Focus chain Z [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain V [auth C] MOL2 format, chain V [auth C] mmCIF format, chain V [auth C]	V [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain V [auth C] Interactions & Density Focus chain V [auth C]
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain DB [auth F] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain KB [auth G] SDF format, chain PA [auth E] SDF format, chain X [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth G] MOL2 format, chain PA [auth E] MOL2 format, chain X [auth C] mmCIF format, chain DB [auth F] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain KB [auth G] mmCIF format, chain PA [auth E] mmCIF format, chain X [auth C]	DB [auth F] K [auth A] KA [auth D] KB [auth G] PA [auth E] DB [auth F], K [auth A], KA [auth D], KB [auth G], PA [auth E], X [auth C]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain DB [auth F] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain PA [auth E] Focus chain X [auth C] Interactions & Density Focus chain DB [auth F] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain PA [auth E] Focus chain X [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain VB [auth H] MOL2 format, chain VB [auth H] mmCIF format, chain VB [auth H]	VB [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain VB [auth H] Interactions & Density Focus chain VB [auth H]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain EB [auth F] SDF format, chain FB [auth F] SDF format, chain GB [auth F] SDF format, chain HB [auth F] SDF format, chain LA [auth D] SDF format, chain LB [auth G] SDF format, chain MA [auth D] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain EB [auth F] MOL2 format, chain FB [auth F] MOL2 format, chain GB [auth F] MOL2 format, chain HB [auth F] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth G] MOL2 format, chain MA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain EB [auth F] mmCIF format, chain FB [auth F] mmCIF format, chain GB [auth F] mmCIF format, chain HB [auth F] mmCIF format, chain LA [auth D] mmCIF format, chain LB [auth G] mmCIF format, chain MA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	EB [auth F] FB [auth F] GB [auth F] HB [auth F] LA [auth D] EB [auth F], FB [auth F], GB [auth F], HB [auth F], LA [auth D], LB [auth G], MA [auth D], T [auth B], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EB [auth F] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain MA [auth D] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain EB [auth F] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain MA [auth D] Focus chain T [auth B] Focus chain U [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain GA [auth D] SDF format, chain VA [auth F] MOL2 format, chain CA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain VA [auth F] mmCIF format, chain CA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain VA [auth F]	CA [auth D], GA [auth D], VA [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain CA [auth D] Focus chain GA [auth D] Focus chain VA [auth F] Interactions & Density Focus chain CA [auth D] Focus chain GA [auth D] Focus chain VA [auth F]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain I [auth A] SDF format, chain IB [auth G] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain NA [auth E] SDF format, chain O [auth B] SDF format, chain OA [auth E] SDF format, chain OB [auth H] SDF format, chain P [auth B] SDF format, chain PB [auth H] SDF format, chain Q [auth B] SDF format, chain QB [auth H] SDF format, chain R [auth B] SDF format, chain RB [auth H] SDF format, chain SA [auth F] SDF format, chain SB [auth H] SDF format, chain TA [auth F] SDF format, chain TB [auth H] SDF format, chain UA [auth F] SDF format, chain W [auth C] SDF format, chain WA [auth F] SDF format, chain XA [auth F] SDF format, chain YA [auth F] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IB [auth G] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth E] MOL2 format, chain OB [auth H] MOL2 format, chain P [auth B] MOL2 format, chain PB [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain QB [auth H] MOL2 format, chain R [auth B] MOL2 format, chain RB [auth H] MOL2 format, chain SA [auth F] MOL2 format, chain SB [auth H] MOL2 format, chain TA [auth F] MOL2 format, chain TB [auth H] MOL2 format, chain UA [auth F] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain YA [auth F] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IB [auth G] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth E] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth E] mmCIF format, chain OB [auth H] mmCIF format, chain P [auth B] mmCIF format, chain PB [auth H] mmCIF format, chain Q [auth B] mmCIF format, chain QB [auth H] mmCIF format, chain R [auth B] mmCIF format, chain RB [auth H] mmCIF format, chain SA [auth F] mmCIF format, chain SB [auth H] mmCIF format, chain TA [auth F] mmCIF format, chain TB [auth H] mmCIF format, chain UA [auth F] mmCIF format, chain W [auth C] mmCIF format, chain WA [auth F] mmCIF format, chain XA [auth F] mmCIF format, chain YA [auth F]	AA [auth D] BA [auth D] DA [auth D] EA [auth D] FA [auth D] AA [auth D], BA [auth D], DA [auth D], EA [auth D], FA [auth D], I [auth A], IB [auth G], J [auth A], N [auth B], NA [auth E], O [auth B], OA [auth E], OB [auth H], P [auth B], PB [auth H], Q [auth B], QB [auth H], R [auth B], RB [auth H], SA [auth F], SB [auth H], TA [auth F], TB [auth H], UA [auth F], W [auth C], WA [auth F], XA [auth F], YA [auth F]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain I [auth A] Focus chain IB [auth G] Focus chain J [auth A] Focus chain N [auth B] Focus chain NA [auth E] Focus chain O [auth B] Focus chain OA [auth E] Focus chain OB [auth H] Focus chain P [auth B] Focus chain PB [auth H] Focus chain Q [auth B] Focus chain QB [auth H] Focus chain R [auth B] Focus chain RB [auth H] Focus chain SA [auth F] Focus chain SB [auth H] Focus chain TA [auth F] Focus chain TB [auth H] Focus chain UA [auth F] Focus chain W [auth C] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain YA [auth F] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain I [auth A] Focus chain IB [auth G] Focus chain J [auth A] Focus chain N [auth B] Focus chain NA [auth E] Focus chain O [auth B] Focus chain OA [auth E] Focus chain OB [auth H] Focus chain P [auth B] Focus chain PB [auth H] Focus chain Q [auth B] Focus chain QB [auth H] Focus chain R [auth B] Focus chain RB [auth H] Focus chain SA [auth F] Focus chain SB [auth H] Focus chain TA [auth F] Focus chain TB [auth H] Focus chain UA [auth F] Focus chain W [auth C] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain YA [auth F]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain BB [auth F] SDF format, chain CB [auth F] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain JB [auth G] SDF format, chain S [auth B] SDF format, chain UB [auth H] SDF format, chain ZA [auth F] MOL2 format, chain AB [auth F] MOL2 format, chain BB [auth F] MOL2 format, chain CB [auth F] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain JB [auth G] MOL2 format, chain S [auth B] MOL2 format, chain UB [auth H] MOL2 format, chain ZA [auth F] mmCIF format, chain AB [auth F] mmCIF format, chain BB [auth F] mmCIF format, chain CB [auth F] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain JB [auth G] mmCIF format, chain S [auth B] mmCIF format, chain UB [auth H] mmCIF format, chain ZA [auth F]	AB [auth F] BB [auth F] CB [auth F] HA [auth D] IA [auth D] AB [auth F], BB [auth F], CB [auth F], HA [auth D], IA [auth D], JA [auth D], JB [auth G], S [auth B], UB [auth H], ZA [auth F]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain BB [auth F] Focus chain CB [auth F] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain S [auth B] Focus chain UB [auth H] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth F] Focus chain BB [auth F] Focus chain CB [auth F] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain S [auth B] Focus chain UB [auth H] Focus chain ZA [auth F]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain WB [auth H] SDF format, chain XB [auth H] MOL2 format, chain WB [auth H] MOL2 format, chain XB [auth H] mmCIF format, chain WB [auth H] mmCIF format, chain XB [auth H]	WB [auth H], XB [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain WB [auth H] Focus chain XB [auth H] Interactions & Density Focus chain WB [auth H] Focus chain XB [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.192 (Depositor), 0.191 (DCC)
R-Value Work: 0.158 (Depositor), 0.158 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.92	α = 90
b = 160.037	β = 90
c = 165.151	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-09-30

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
Global Health Innovative Technology Fund	United States	--

Revision History (Full details and data files)

Version 1.0: 2020-09-30
Type: Initial release
Version 1.1: 2022-08-31
Changes: Advisory, Database references, Structure summary
Version 1.2: 2023-02-01
Changes: Advisory
Version 1.3: 2023-10-25
Changes: Data collection, Refinement description