6U6C

Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and GSK2-bound form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

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Ligand Structure Quality Assessment 


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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

  • DOI: 10.1002/pro.3825
  • Primary Citation of 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 ...

    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: 

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophan synthase alpha chainA, C, E, G276Mycobacterium tuberculosis H37RvMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFY1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophan synthase beta chainB, D, F, H410Mycobacterium tuberculosis H37RvMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFX9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 12 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PZV (Subject of Investigation/LOI)
Query on PZV
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BE [auth H],
IB [auth D],
KC [auth F],
U [auth B]		1-(2-fluorobenzene-1-carbonyl)-N-methyl-2,3-dihydro-1H-indole-5-sulfonamide
C16 H15 F N2 O3 S
MLAUXXOCJYXBIG-UHFFFAOYSA-N		 Ligand Interaction
P1T (Subject of Investigation/LOI)
Query on P1T
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DE [auth H],
MB [auth D],
NC [auth F],
V [auth B]		2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID
C11 H15 N2 O7 P
BXUDKFHCAMQSRX-UHFFFAOYSA-N		 Ligand Interaction
EPE
Query on EPE
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FF [auth H],
MD [auth F],
UA [auth B],
XA [auth B]		4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N		 Ligand Interaction
PGE
Query on PGE
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JC [auth F],
RC [auth F]		TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N		 Ligand Interaction
PEG
Query on PEG
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LD [auth F],
ME [auth H],
VD [auth G],
Z [auth B]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
MLI
Query on MLI
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DF [auth H],
FB [auth C],
FC [auth E],
JD [auth F],
S [auth A],
DF [auth H],
FB [auth C],
FC [auth E],
JD [auth F],
S [auth A],
XD [auth G]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L		 Ligand Interaction
ALA
Query on ALA
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EC [auth E]ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N		 Ligand Interaction
EDO
Query on EDO
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BB [auth C],
BC [auth D],
BD [auth F],
CA [auth B],
DA [auth B],
BB [auth C],
BC [auth D],
BD [auth F],
CA [auth B],
DA [auth B],
EA [auth B],
EB [auth C],
ED [auth F],
EE [auth H],
GF [auth H],
IC [auth E],
JA [auth B],
L [auth A],
LE [auth H],
SB [auth D],
TA [auth B],
TE [auth H],
UC [auth F],
UE [auth H],
W [auth B],
WA [auth B],
WD [auth G],
YD [auth G],
ZA [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
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AD [auth F],
FE [auth H],
QC [auth F],
R [auth A],
T [auth A]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
FMT
Query on FMT
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AA [auth B],
AB [auth C],
AE [auth H],
AF [auth H],
BA [auth B],
AA [auth B],
AB [auth C],
AE [auth H],
AF [auth H],
BA [auth B],
BF [auth H],
CB [auth C],
CC [auth D],
CD [auth F],
CE [auth H],
CF [auth H],
DB [auth C],
DD [auth F],
FA [auth B],
FD [auth F],
GA [auth B],
GC [auth E],
GD [auth F],
GE [auth H],
HA [auth B],
HB [auth C],
HC [auth E],
HE [auth H],
I [auth A],
IA [auth B],
IE [auth H],
J [auth A],
JB [auth D],
JE [auth H],
K [auth A],
KA [auth B],
KB [auth D],
KD [auth F],
KE [auth H],
LA [auth B],
LB [auth D],
LC [auth F],
M [auth A],
MA [auth B],
MC [auth F],
N [auth A],
NA [auth B],
NB [auth D],
ND [auth G],
NE [auth H],
O [auth A],
OA [auth B],
OB [auth D],
OC [auth F],
OD [auth G],
OE [auth H],
P [auth A],
PA [auth B],
PB [auth D],
PC [auth F],
PD [auth G],
PE [auth H],
Q [auth A],
QA [auth B],
QB [auth D],
QD [auth G],
QE [auth H],
RA [auth B],
RB [auth D],
RD [auth G],
RE [auth H],
SC [auth F],
SD [auth G],
SE [auth H],
TB [auth D],
TC [auth F],
TD [auth G],
UB [auth D],
UD [auth G],
VA [auth B],
VB [auth D],
VC [auth F],
VE [auth H],
WB [auth D],
WC [auth F],
WE [auth H],
X [auth B],
XB [auth D],
XC [auth F],
XE [auth H],
Y [auth B],
YA [auth B],
YB [auth D],
YC [auth F],
YE [auth H],
ZC [auth F],
ZE [auth H]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
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AC [auth D],
DC [auth D],
EF [auth H],
GB [auth C],
ID [auth F],
AC [auth D],
DC [auth D],
EF [auth H],
GB [auth C],
ID [auth F],
SA [auth B],
ZB [auth D],
ZD [auth G]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
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HD [auth F]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.106α = 90
b = 159.226β = 90
c = 164.973γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Global Health Innovative Technology FundUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references