Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 173.93 kDa 
• Atom Count: 13321 
• Modelled Residue Count: 1528 
• Deposited Residue Count: 1528 
• Unique protein chains: 1

1WXX

Crystal structure of Tt1595, a putative SAM-dependent methyltransferase from Thermus thermophillus HB8

• PDB DOI: 10.2210/pdb1WXX/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-02-02 Released: 2005-08-02 
• Deposition Author(s): Pioszak, A.A., Murayama, K., Nakagawa, N., Ebihara, A., Kuramitsu, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.229 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 

Literature

Structures of a putative RNA 5-methyluridine methyltransferase, Thermus thermophilus TTHA1280, and its complex with S-adenosyl-L-homocysteine.

Pioszak, A.A., Murayama, K., Nakagawa, N., Ebihara, A., Kuramitsu, S., Shirouzu, M., Yokoyama, S.

(2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 867-874

• PubMed: 16511182 
• DOI: 10.1107/S1744309105029842
• Primary Citation of Related Structures:  
  1WXW, 1WXX, 2CWW


• PubMed Abstract: 
  

The Thermus thermophilus hypothetical protein TTHA1280 belongs to a family of predicted S-adenosyl-L-methionine (AdoMet) dependent RNA methyltransferases (MTases) present in many bacterial and archaeal species. Inspection of amino-acid sequence motifs common to class I Rossmann-fold-like MTases suggested a specific role as an RNA 5-methyluridine MTase. Selenomethionine (SeMet) labelled and native versions of the protein were expressed, purified and crystallized. Two crystal forms of the SeMet-labelled apoprotein were obtained: SeMet-ApoI and SeMet-ApoII. Cocrystallization of the native protein with S-adenosyl-L-homocysteine (AdoHcy) yielded a third crystal form, Native-AdoHcy. The SeMet-ApoI structure was solved by the multiple anomalous dispersion method and refined at 2.55 A resolution. The SeMet-ApoII and Native-AdoHcy structures were solved by molecular replacement and refined at 1.80 and 2.60 A, respectively. TTHA1280 formed a homodimer in the crystals and in solution. Each subunit folds into a three-domain structure composed of a small N-terminal PUA domain, a central alpha/beta-domain and a C-terminal Rossmann-fold-like MTase domain. The three domains form an overall clamp-like shape, with the putative active site facing a deep cleft. The architecture of the active site is consistent with specific recognition of uridine and catalysis of methyl transfer to the 5-carbon position. The cleft is suitable in size and charge distribution for binding single-stranded RNA.

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Organizational Affiliation: 

RIKEN Genomic Sciences Center, Yokohama, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein TTHA1280	A, B, C, D	382	Thermus thermophilus HB8	Mutation(s): 4  Gene Names: TTHA1280
UniProt
Find proteins for Q5SIT4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIT4  Go to UniProtKB:  Q5SIT4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], O [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	E [auth A], K [auth B], N [auth C], P [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.229 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.551	α = 96.34
b = 82.318	β = 90.14
c = 79.616	γ = 103.06

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-02-02 
• Released Date: 2005-08-02 
Deposition Author(s): Pioszak, A.A., Murayama, K., Nakagawa, N., Ebihara, A., Kuramitsu, S., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-08-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance