4QYS | pdb_00004qys

TrpB2 enzymes

• PDB DOI: https://doi.org/10.2210/pdb4QYS/pdb

• Classification: LYASE
• Organism(s): Saccharolobus solfataricus P2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-25 Released: 2015-02-18 
• Deposition Author(s): Busch, F., Rajendran, C., Loeffler, P., Merkl, R., Sterner, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

TrpB2 enzymes are O-phospho-l-serine dependent tryptophan synthases

Busch, F., Rajendran, C., Mayans, O., Loffler, P., Merkl, R., Sterner, R.

(2014) Biochemistry 53: 6078-6083

• PubMed: 25184516 
• DOI: https://doi.org/10.1021/bi500977y
• Primary Citation of Related Structures:  
  4QYS


• PubMed Abstract: 
  

  The rapid increase of the number of sequenced genomes asks for the functional annotation of the encoded enzymes. We used a combined computational-structural approach to determine the function of the TrpB2 subgroup of the tryptophan synthase β chain/β chain-like TrpB1-TrpB2 family (IPR023026). The results showed that TrpB2 enzymes are O-phospho-l-serine dependent tryptophan synthases, whereas TrpB1 enzymes catalyze the l-serine dependent synthesis of tryptophan. We found a single residue being responsible for the different substrate specificities of TrpB1 and TrpB2 and confirmed this finding by mutagenesis studies and crystallographic analysis of a TrpB2 enzyme with bound O-phospho-l-serine.

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Organizational Affiliation: 

Institute of Biophysics and Physical Biochemistry, University of Regensburg , Universitätsstrasse 31, D-93053 Regensburg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 99.39 kDa 
• Atom Count: 6,708 
• Modelled Residue Count: 826 
• Deposited Residue Count: 884 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase beta chain 2	A [auth B], B [auth A]	442	Saccharolobus solfataricus P2	Mutation(s): 0  Gene Names: trpB2, SSO1145 EC: 4.2.1.20
UniProt
Find proteins for Q97TX6 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97TX6  Go to UniProtKB:  Q97TX6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	D [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PLR	C [auth B]	(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE C8 H12 N O5 P RBCOYOYDYNXAFA-UHFFFAOYSA-N
SEP	E [auth A]	PHOSPHOSERINE C3 H8 N O6 P BZQFBWGGLXLEPQ-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.564	α = 90
b = 61.903	β = 98.23
c = 109.574	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-18 
Deposition Author(s): Busch, F., Rajendran, C., Loeffler, P., Merkl, R., Sterner, R.

Revision History  

• Version 1.0: 2015-02-18
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations