7MT6

Crystal structure of tryptophan synthase in complex with F9, Cs+, benzimidazole, pH7.8 - alpha aminoacrylate form - E(A-A)(BZI)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.160 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase alpha-aminoacrylate intermediate.

Holmes, J.B.Liu, V.Caulkins, B.G.Hilario, E.Ghosh, R.K.Drago, V.N.Young, R.P.Romero, J.A.Gill, A.D.Bogie, P.M.Paulino, J.Wang, X.Riviere, G.Bosken, Y.K.Struppe, J.Hassan, A.Guidoulianov, J.Perrone, B.Mentink-Vigier, F.Chang, C.A.Long, J.R.Hooley, R.J.Mueser, T.C.Dunn, M.F.Mueller, L.J.

(2022) Proc Natl Acad Sci U S A 119

  • DOI: https://doi.org/10.1073/pnas.2109235119
  • Primary Citation of Related Structures:  
    7MT4, 7MT5, 7MT6

  • PubMed Abstract: 

    NMR-assisted crystallography-the integrated application of solid-state NMR, X-ray crystallography, and first-principles computational chemistry-holds significant promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in enzyme active sites, including hydrogen atom locations and tautomeric equilibria, NMR crystallography offers insight into both structure and chemical dynamics. Here, this integrated approach is used to characterize the tryptophan synthase α-aminoacrylate intermediate, a defining species for pyridoxal-5'-phosphate-dependent enzymes that catalyze β-elimination and replacement reactions. For this intermediate, NMR-assisted crystallography is able to identify the protonation states of the ionizable sites on the cofactor, substrate, and catalytic side chains as well as the location and orientation of crystallographic waters within the active site. Most notable is the water molecule immediately adjacent to the substrate β-carbon, which serves as a hydrogen bond donor to the ε-amino group of the acid-base catalytic residue βLys87. From this analysis, a detailed three-dimensional picture of structure and reactivity emerges, highlighting the fate of the L-serine hydroxyl leaving group and the reaction pathway back to the preceding transition state. Reaction of the α-aminoacrylate intermediate with benzimidazole, an isostere of the natural substrate indole, shows benzimidazole bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the benzimidazole position, indole is positioned with C3 in contact with the α-aminoacrylate C β and aligned for nucleophilic attack. Here, the chemically detailed, three-dimensional structure from NMR-assisted crystallography is key to understanding why benzimidazole does not react, while indole does.


  • Organizational Affiliation

    Department of Chemistry, University of California, Riverside, CA 92521.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophan synthase alpha chain268Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: trpADD95_04145
EC: 4.2.1.20
UniProt
Find proteins for P00929 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P00929 
Go to UniProtKB:  P00929
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00929
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophan synthase beta chain397Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: trpB
EC: 4.2.1.20
UniProt
Find proteins for P0A2K1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P0A2K1 
Go to UniProtKB:  P0A2K1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A2K1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F9F
Query on F9F

Download Ideal Coordinates CCD File 
C [auth A]2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE
C9 H11 F3 N O7 P S
JDDKDMFCTOZVCJ-UHFFFAOYSA-N
0JO
Query on 0JO

Download Ideal Coordinates CCD File 
D [auth B]2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid
C11 H13 N2 O7 P
BHIGINKEEFZJGX-YIXHJXPBSA-N
CS
Query on CS

Download Ideal Coordinates CCD File 
E [auth B],
F [auth B]
CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
BZI
Query on BZI

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B]
BENZIMIDAZOLE
C7 H6 N2
HYZJCKYKOHLVJF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.160 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.96α = 90
b = 60.96β = 94.58
c = 67.4101γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

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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 StatesGM137008

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-29
    Type: Initial release
  • Version 1.1: 2022-01-19
    Changes: Database references
  • Version 1.2: 2022-01-26
    Changes: Structure summary
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description