3VSE

Crystal structure of methyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

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Literature

Crystal structure of a putative methyltransferase SAV1081 from Staphylococcus aureus

Kita, S.Tanaka, Y.Hirano, N.Kimura, S.Suzuki, T.Suzuki, T.Yao, M.Tanaka, I.

(2012) Protein Pept Lett 20: 530-537

  • DOI: 10.2174/0929866511320050006
  • Primary Citation of Related Structures:  
    3VSE

  • PubMed Abstract: 
  • Cluster of Orthologous Groups (COG) 1092 contains two distinct types of methylation enzyme from Escherichia coli, YccW and YcbY. YccW is a 5-methylcytosine methyltransferase (m5C MTase) responsible for m5C 1962 in 23S rRNA, whereas YcbY is a dimethyltransferase, of which N- and C-terminal domains are responsible for N2- methylguanosine (m2G) 2445 and 7-methylguanosine (m7G) 2069 in 23S rRNA, respectively ...

    Cluster of Orthologous Groups (COG) 1092 contains two distinct types of methylation enzyme from Escherichia coli, YccW and YcbY. YccW is a 5-methylcytosine methyltransferase (m5C MTase) responsible for m5C 1962 in 23S rRNA, whereas YcbY is a dimethyltransferase, of which N- and C-terminal domains are responsible for N2- methylguanosine (m2G) 2445 and 7-methylguanosine (m7G) 2069 in 23S rRNA, respectively. However, proteins in COG1092 other than YccW and YcbY remain functionally unidentified. SAV1081 from Staphylococcus aureus is one of the functionally unassigned proteins of COG1092. Although SAV1081 has an identical domain organization to YccW with 26% sequence identity, it lacks the catalytic cysteine residue essential for m5C formation activity. In the present study, we determined the crystal structure of SAV1081 and compared it with those of other COG1092 proteins. Based on the structure characteristics, such as the presence or absence of the catalytic cysteine residue, β-hairpin structure, and oligomeric state, as well as domain organization, we propose a functional classification of COG1092 proteins.


    Organizational Affiliation

    Graduate School of Life Sciences, Hokkaido University, Sapporo, 060-0810, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative uncharacterized proteinA, B, C, D398Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: SAV1081
UniProt
Find proteins for A0A0H3JYW8 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore A0A0H3JYW8 
Go to UniProtKB:  A0A0H3JYW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JYW8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.485α = 90
b = 91.573β = 94.03
c = 102.631γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
BALBESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-10
    Type: Initial release