5IXJ | pdb_00005ixj

Tryptophan Synthase beta-subunit from Pyrococcus furiosus with L-threonine non-covalently bound in the active site

PDB DOI: https://doi.org/10.2210/pdb5IXJ/pdb

Classification: LYASE
Organism(s): Pyrococcus furiosus DSM 3638
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-03-23 Released: 2016-08-17
Deposition Author(s): Buller, A.R., Herger, M., Arnold, F.H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.195 (Depositor), 0.210 (DCC)
R-Value Work:
0.175 (Depositor), 0.190 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Synthesis of beta-Branched Tryptophan Analogues Using an Engineered Subunit of Tryptophan Synthase.

Herger, M., van Roye, P., Romney, D.K., Brinkmann-Chen, S., Buller, A.R., Arnold, F.H.

(2016) J Am Chem Soc 138: 8388-8391

PubMed: 27355405 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/jacs.6b04836
Primary Citation of Related Structures:
5IXJ

PubMed Abstract:
We report that l-threonine may substitute for l-serine in the β-substitution reaction of an engineered subunit of tryptophan synthase from Pyrococcus furiosus, yielding (2S,3S)-β-methyltryptophan (β-MeTrp) in a single step. The trace activity of the wild-type β-subunit on this substrate was enhanced more than 1000-fold by directed evolution. Structural and spectroscopic data indicate that this increase is correlated with stabilization of the electrophilic aminoacrylate intermediate. The engineered biocatalyst also reacts with a variety of indole analogues and thiophenol for diastereoselective C-C, C-N, and C-S bond-forming reactions. This new activity circumvents the 3-enzyme pathway that produces β-MeTrp in nature and offers a simple and expandable route to preparing derivatives of this valuable building block.

Organizational Affiliation

Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States.

Macromolecule Content

Total Structure Weight: 176.11 kDa
Atom Count: 12,924
Modelled Residue Count: 1,550
Deposited Residue Count: 1,584
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase beta chain 1	A, B, C, D	396	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: trpB1, PF1706 EC: 4.2.1.20
UniProt
Find proteins for Q8U093 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U093 Go to UniProtKB: Q8U093
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8U093
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
THR Query on THR Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	THREONINE C₄ H₉ N O₃ AYFVYJQAPQTCCC-GBXIJSLDSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B, C, D	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.195 (Depositor), 0.210 (DCC)
R-Value Work: 0.175 (Depositor), 0.190 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.718	α = 90
b = 112.367	β = 90
c = 160.31	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-08-17

Deposition Author(s):

Buller, A.R.

Herger, M.

Arnold, F.H.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1F32GM110851-01A1

Revision History (Full details and data files)

Version 1.0: 2016-08-17
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2019-12-25
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection