4FC8 | pdb_00004fc8

Crystal structure of transcription regulator protein Rtr1 from Kluyveromyces lactis

• PDB DOI: https://doi.org/10.2210/pdb4FC8/pdb

• Classification: TRANSCRIPTION
• Organism(s): Kluyveromyces lactis NRRL Y-1140
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-05-24 Released: 2012-07-25 
• Deposition Author(s): Xiang, K., Tong, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

The yeast regulator of transcription protein Rtr1 lacks an active site and phosphatase activity.

Xiang, K., Manley, J.L., Tong, L.

(2012) Nat Commun 3: 946-946

• PubMed: 22781759 
• DOI: https://doi.org/10.1038/ncomms1947
• Primary Citation of Related Structures:  
  4FC8


• PubMed Abstract: 
  

  The activity of RNA polymerase II (Pol II) is controlled in part by the phosphorylation state of the C-terminal domain (CTD) of its largest subunit. Recent reports have suggested that yeast regulator of transcription protein, Rtr1, and its human homologue RPAP2, possess Pol II CTD Ser5 phosphatase activity. Here we report the crystal structure of Kluyveromyces lactis Rtr1, which reveals a new type of zinc finger protein and does not have any close structural homologues. Importantly, the structure does not show evidence of an active site, and extensive experiments to demonstrate its CTD phosphatase activity have been unsuccessful, suggesting that Rtr1 has a non-catalytic role in CTD dephosphorylation.

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Organizational Affiliation: 

Department of Biological Sciences, Columbia University, New York 10027, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.69 kDa 
• Atom Count: 2,280 
• Modelled Residue Count: 272 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
transcription protein Rtr1	A, B	219	Kluyveromyces lactis NRRL Y-1140	Mutation(s): 0  Gene Names: KLLA0F12672g, KLLA0_F12672g EC: 3.1.3.16
UniProt
Find proteins for Q6CK86 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore Q6CK86  Go to UniProtKB:  Q6CK86

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.168	α = 90
b = 88.734	β = 90
c = 94.803	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-25 
Deposition Author(s): Xiang, K., Tong, L.

Revision History  

• Version 1.0: 2012-07-25
  Type: Initial release
  
• Version 1.1: 2012-08-01
  Changes: Data collection
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations