Modomics - A Database of RNA Modifications

ID Card:

Full name: YrdC-like domain-containing protein
Synonym: smu.1377c
GI: 24379784
COG: COG0009
UniProt: Q8DTG7
Structures: | 3L7V |
Alpha Fold Predicted Structure: AF-Q8DTG7-F1
Enzyme type: threonylcarbamoyladenosine synthetase predicted


PDB Structures:


3L7V

Structure Description:

Title: Crystal structure of a hypothetical protein smu.1377c from Streptococcus mutans UA159
Classification: TRANSCRIPTION
Technique: X-Ray Diffraction
Resolution: 2.26
R value free: 0.259
R value observed: 0.196
R value work: 0.196

Abstract of the PDB Structure's related Publication:

Members of the Sua5_YciO_YrdC protein family are found in both eukaryotes and prokaryotes and possess a conserved alpha/beta twisted open-sheet fold. The Escherichia coli protein YrdC has been shown to be involved in modification of tRNA. The crystal structure of smu.1377c, a hypothetical protein from Streptococcus mutans, has been determined to 2.25 A resolution. From structure analysis and comparison, it is shown that smu.1377c is a member of the Sua5_YciO_YrdC family and that it may play the same role as E. coli YrdC.

Download RCSB-PDB Structures:

Pdb Files   3L7V.pdb  
Pdbx/mmCIF Files   3L7V.cif  


Protein sequence:

MTKHIHWDGNLSQEGFEIVKGEGGVIVCPTKVGYIIMTSDKKGLERKFEAKKRNRNKPGVVLCGSMEELRALAQLTPEIDAFYQKHWDEDILLGCILPWKAEAYEKLKAYGDGREELMTDIRGTSCFVIKFGVAGEQIAKEMWEKEGRMVYASSANPSGKGNRGKVEGIGERIESMVDLVIEADDYVASIQPDKTIETRYEQGVMVSMVDKDGKLIPQQGADSRSVEPCPVVIRKGLDIDKIMMHLSDQFNSWNYRQGEYY

Comments:

The putative function of this protein came only from its homology to bacterial/Eukaryal/Archaeal TsaC/Sua5 homologs.





Alpha Fold Predicted Structure:




Parsing response... [248329/248329]


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Protein sequence:

M T K H I H W D G N L S Q E G F E I V K G E G G V I V C P T K V G Y I I M T S D K K G L E R K F E A K K R N R N K P G V V L C G S M E E L R A L A Q L T P E I D A F Y Q K H W D E D I L L G C I L P W K A E A Y E K L K A Y G D G R E E L M T D I R G T S C F V I K F G V A G E Q I A K E M W E K E G R M V Y A S S A N P S G K G N R G K V E G I G E R I E S M V D L V I E A D D Y V A S I Q P D K T I E T R Y E Q G V M V S M V D K D G K L I P Q Q G A D S R S V E P C P V V I R K G L D I D K I M M H L S D Q F N S W N Y R Q G E Y Y
20406080100120140160180200220240260SequenceGHTBSN

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-Q8DTG7-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q8DTG7-F1.cif  
DSSP Secondary Structures   Q8DTG7.dssp  





Publications: