Modomics - A Database of RNA Modifications

ID Card:

Full name: Diphthamide biosynthesis protein 3
Synonym: DPH3
GI: 21648335
COG: COG5216
UniProt: Q3E840
Structures: | 1YOP | 1YWS | 4D4P | 4D4O |
Alpha Fold Predicted Structure: AF-Q3E840-F1


PDB Structures:


1YOP

Structure Description:

Title: The solution structure of Kti11p
Classification: METAL BINDING PROTEIN
Technique: NMR Solution
Resolution:
Conformers calculated: 100
Conformers submitted: 20
Selection criteria:

Abstract of the PDB Structure's related Publication:

Kti11p is a small, highly conserved CSL zinc finger-containing protein found in many eukaryotes. It was first identified as one of the factors required for maintaining the sensitivity of Saccharomyces cerevisiae to Kluyveromyces lactis zymocin. Then, it was found to be identical to Dph3, a protein required for diphthamide biosynthesis on eEF-2, the target of diphtheria toxin and Pseudomonas exotoxin A, in both yeast and higher eukaryotes. Furthermore, Kti11p/Dph3 was found to physically interact with core-Elongator, ribosomal proteins, eEF-2, two other proteins required for diphthamide modification on eEF-2, and DelGEF. Here, we determined the solution structure of Kti11p using NMR, providing the first structure of the CSL-class zinc-binding protein family. We present the first experimental evidence that Kti11p can bind a single Zn(2+) ion by its four conserved cysteine residues. The major structure of Kti11p comprises a beta sandwich as well as an alpha helix. Moreover, a structure-based similarity search suggests that it represents a novel structure and may define a new family of the zinc ribbon fold group. Therefore, our work provides a molecular basis for further understanding the multiple functions of Kti11p/Dph3 in different biological processes.

Download RCSB-PDB Structures:

Pdb Files   1YOP.pdb   1YWS.pdb   4D4O.pdb   4D4P.pdb  
Pdbx/mmCIF Files   1YOP.cif   1YWS.cif   4D4O.cif   4D4P.cif  


Protein sequence:

MSTYDEIEIEDMTFEPENQMFTYPCPCGDRFQIYLDDMFEGEKVAVCPSCSLMIDVVFDKEDLAEYYEEAGIHPPEPIAAAA

Comments:

One of the many protein cofactors required for an early step in synthesis of 5-methoxycarbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) groups present on uridines at the wobble position in tRNA. The enzyme that catalyzes this reaction is still unknown (2012).





Alpha Fold Predicted Structure:




Parsing response... [82424/82424]


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Protein sequence:

M S T Y D E I E I E D M T F E P E N Q M F T Y P C P C G D R F Q I Y L D D M F E G E K V A V C P S C S L M I D V V F D K E D L A E Y Y E E A G I H P P E P I A A A A
1020304050607080MSTYDEIEIEDMTFEPENQMFTYPCPCGDRFQIYLDDMFEGEKVAVCPSCSLMIDVVFDKEDLAEYYEEAGIHPPEPIAAAASequenceGHTSN

Enter the variants

Position

Original

Variant

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-Q3E840-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q3E840-F1.cif  
DSSP Secondary Structures   Q3E840.dssp  





Publications:

Links:

_PubMed_