2IU6 | pdb_00002iu6

REGULATION OF THE DHA OPERON OF LACTOCOCCUS LACTIS

• PDB DOI: https://doi.org/10.2210/pdb2IU6/pdb

• Classification: TRANSFERASE
• Organism(s): Lactococcus lactis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-05-27 Released: 2006-06-13 
• Deposition Author(s): Srinivas, A., Christen, S., Baumann, U., Erni, B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.198 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Regulation of the Dha Operon of Lactococcus Lactis: A Deviation from the Rule Followed by the Tetr Family of Transcription Regulators

Christen, S., Srinivas, A., Bahler, P., Zeller, A., Pridmore, D., Bieniossek, C., Baumann, U., Erni, B.

(2006) J Biological Chem 281: 23129

• PubMed: 16760471 
• DOI: https://doi.org/10.1074/jbc.M603486200
• Primary Citation Related Structures: 
  2IU4, 2IU5, 2IU6


• PubMed Abstract: 
  

  Dihydroxyacetone (Dha) kinases are a novel family of kinases with signaling and metabolic functions. Here we report the x-ray structures of the transcriptional activator DhaS and the coactivator DhaQ and characterize their function. DhaQ is a paralog of the Dha binding Dha kinase subunit; DhaS belongs to the family of TetR repressors although, unlike all known members of this family, it is a transcriptional activator. DhaQ and DhaS form a stable complex that in the presence of Dha activates transcription of the Lactococcus lactis dha operon. Dha covalently binds to DhaQ through a hemiaminal bond with a histidine and thereby induces a conformational change, which is propagated to the surface via a cantilever-like structure. DhaS binding protects an inverted repeat whose sequence is GGACACATN6ATTTGTCC and renders two GC base pairs of the operator DNA hypersensitive to DNase I cleavage. The proximal half-site of the inverted repeat partially overlaps with the predicted -35 consensus sequence of the dha promoter.

---

Organizational Affiliation: 
• Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.

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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 74.88 kDa 
• Atom Count: 5,271 
• Modeled Residue Count: 638 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROXYACETONE KINASE	A, B	336	Lactococcus lactis	Mutation(s): 0  EC: 2.7.1.2
UniProt
Find proteins for Q9CIW0 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q9CIW0  Go to UniProtKB:  Q9CIW0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.198 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.09	α = 90
b = 101.09	β = 90
c = 148.6	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-13 
Deposition Author(s): Srinivas, A., Christen, S., Baumann, U., Erni, B.

Revision History  

• Version 1.0: 2006-06-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description