5T6M

Structure of the tryptophan synthase b-subunit from Pyroccus furiosus with b-methyltryptophan non-covalently bound

PDB DOI: https://doi.org/10.2210/pdb5T6M/pdb

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

Deposited: 2016-09-01 Released: 2016-12-21
Deposition Author(s): Buller, A.R., van Roye, P., 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: 1.80 Å
R-Value Free: 0.238
R-Value Work: 0.204
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Tryptophan Synthase Uses an Atypical Mechanism To Achieve Substrate Specificity.

Buller, A.R., van Roye, P., Murciano-Calles, J., Arnold, F.H.

(2016) Biochemistry 55: 7043-7046

PubMed: 27935677 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acs.biochem.6b01127
Primary Citation of Related Structures:
5T6M

PubMed Abstract:
Tryptophan synthase (TrpS) catalyzes the final steps in the biosynthesis of l-tryptophan from l-serine (Ser) and indole-3-glycerol phosphate (IGP). We report that native TrpS can also catalyze a productive reaction with l-threonine (Thr), leading to (2S,3S)-β-methyltryptophan. Surprisingly, β-substitution occurs in vitro with a 3.4-fold higher catalytic efficiency for Ser over Thr using saturating indole, despite a >82000-fold preference for Ser in direct competition using IGP. Structural data identify a novel product binding site, and kinetic experiments clarify the atypical mechanism of specificity: Thr binds efficiently but decreases the affinity for indole and disrupts the allosteric signaling that regulates the catalytic cycle.

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: 176.48 kDa
Atom Count: 12,028
Modelled Residue Count: 1,542
Deposited Residue Count: 1,584
Unique protein chains: 1

Macromolecules

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(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	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
78U Query on 78U Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain M [auth D] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D]	H [auth B], J [auth C], M [auth D]	(betaS)-beta-methyl-L-tryptophan C₁₂ H₁₄ N₂ O₂ CZSQAYAIWDEOSA-CPCISQLKSA-N		Interactions Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain H [auth B] Focus chain J [auth C] Focus chain M [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth D]	F [auth A], L [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-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]

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: 1.80 Å
R-Value Free: 0.238
R-Value Work: 0.204
R-Value Observed: 0.206
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.819	α = 90
b = 107.705	β = 90
c = 160.061	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-12-21

Deposition Author(s):

Buller, A.R.

van Roye, P.

Arnold, F.H.

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

Revision History (Full details and data files)

Version 1.0: 2016-12-21
Type: Initial release
Version 1.1: 2017-01-11
Changes: Database references
Version 1.2: 2017-09-27
Changes: Author supporting evidence
Version 1.3: 2019-12-25
Changes: Author supporting evidence
Version 1.4: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2023-11-15
Changes: Data collection