PDBsum entry 5dw3

Lyase

PDB id: 5dw3

Contents

Protein chains

383 a.a.

Ligands

TRP ×2

TRP-PO4 ×2

Metals

_NA ×4

Waters ×301

PDB id:

5dw3

Name:

Lyase

Title:

Tryptophan synthase beta-subunit from pyrococcus furiosus with product l-tryptophan non-covalently bound in the active site

Structure:

Tryptophan synthase beta chain 1. Chain: a, b, c, d. Engineered: yes

Source:

Pyrococcus furiosus (strain atcc 43587 / dsm 3638 / jcm 8422 / vc1). Organism_taxid: 186497. Strain: atcc 43587 / dsm 3638 / jcm 8422 / vc1. Gene: trpb1, pf1706. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.74Å R-factor: 0.187 R-free: 0.224

Authors:

A.R.Buller,F.H.Arnold

Key ref:

A.R.Buller et al. (2015). Directed evolution of the tryptophan synthase β-subunit for stand-alone function recapitulates allosteric activation. Proc Natl Acad Sci U S A, 112, 14599-14604. PubMed id: 26553994 DOI: 10.1073/pnas.1516401112

Date:

22-Sep-15 Release date: 11-Nov-15

Protein chains

Q8U093  (TRPB1_PYRFU) -  Tryptophan synthase beta chain 1 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 388 a.a.

Struc: 383 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.4.2.1.20 - tryptophan synthase.
• Pathway: Tryptophan Biosynthesis
• Reaction: (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + L-tryptophan + H2O

(1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate (Bound ligand (Het Group name = PO4) matches with 50.00% similarity) + L-tryptophan (Bound ligand (Het Group name = TRP) corresponds exactly) + H2O

• Cofactor: Pyridoxal 5'-phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.1516401112

Proc Natl Acad Sci U S A 112:14599-14604 (2015)

PubMed id: 26553994

Directed evolution of the tryptophan synthase β-subunit for stand-alone function recapitulates allosteric activation.

A.R.Buller, S.Brinkmann-Chen, D.K.Romney, M.Herger, J.Murciano-Calles, F.H.Arnold.

ABSTRACT

Enzymes in heteromeric, allosterically regulated complexes catalyze a rich array of chemical reactions. Separating the subunits of such complexes, however, often severely attenuates their catalytic activities, because they can no longer be activated by their protein partners. We used directed evolution to explore allosteric regulation as a source of latent catalytic potential using the β-subunit of tryptophan synthase from Pyrococcus furiosus (PfTrpB). As part of its native αββα complex, TrpB efficiently produces tryptophan and tryptophan analogs; activity drops considerably when it is used as a stand-alone catalyst without the α-subunit. Kinetic, spectroscopic, and X-ray crystallographic data show that this lost activity can be recovered by mutations that reproduce the effects of complexation with the α-subunit. The engineered PfTrpB is a powerful platform for production of Trp analogs and for further directed evolution to expand substrate and reaction scope.