Modomics - A Database of RNA Modifications

ID Card:

Full name: EKC/KEOPS complex subunit CGI121
Synonym: YML036w
GI: 154199620
COG: COG1617
UniProt: Q03705
Structures: | 4WW5 | 4WW7 | 4WW9 | 4WWA | 4XAH |
Alpha Fold Predicted Structure: AF-Q03705-F1
Complex: EKC/KEOPS
Enzyme type: pseudouridine synthase
Position of modification - modification: t:37 - t6A


PDB Structures:


4WW5

Structure Description:

Title: Crystal structure of binary complex Bud32-Cgi121 in complex with AMPP
Classification: TRANSFERASE
Technique: X-Ray Diffraction
Resolution: 2.0
R value free: 0.222
R value observed: 0.185
R value work: 0.183

Abstract of the PDB Structure's related Publication:

The yeast KEOPS protein complex comprising Kae1, Bud32, Cgi121, Pcc1 and Gon7 is responsible for the essential tRNA threonylcarbamoyladenosine (t(6)A) modification. Deletion of genes coding for the KEOPS subunits also affects telomere elongation and transcriptional regulation. In the present work, the crystal structure of Bud32/Cgi121 in complex with ADP revealed that ADP is bound in the catalytic site of Bud32 in a canonical manner characteristic of Protein Kinase A (PKA) family proteins. We found that Gon7 forms a stable heterodimer with Pcc1 and report the crystal structure of the Pcc1-Gon7 heterodimer. Gon7 interacts with the same Pcc1 region engaged in the archaeal Pcc1 homodimer. We further show that yeast KEOPS, unlike its archaeal counterpart, exists as a heteropentamer in which Gon7, Pcc1, Kae1, Bud32 and Cgi121 also adopt a linear arrangement. We constructed a model of yeast KEOPS that provides structural insight into the role of Gon7. The model also revealed the presence of a highly positively charged crater surrounding the entrance of Kae1 that likely binds tRNA.

Download RCSB-PDB Structures:

Pdb Files   4WW5.pdb   4WW7.pdb   4WW9.pdb   4WWA.pdb   4XAH.pdb  
Pdbx/mmCIF Files   4WW5.cif   4WW7.cif   4WW9.cif   4WWA.cif   4XAH.cif  


Protein sequence:

MVVSIIPQFPDIKVSLALFEQVKNAKEIRSKMSELSTSFAFIDPRLVCSGEQMYSAIYKTLIEVKYNKMRTRNLNSECVLCLSPTSNISDAFLKFGIKDDSSQLICLKFHTNTDDVDKEQLRTIMTSIVKGQEIEFNDDNLSRFYDEALIRKIYKLSDDFKPQDVNGLSRALVDAIQLRGV

Comments:

Kinase, Endopeptidase, and other Protein of Small size (KEOPS) protein complex consists of the five Bud32, Cgi121, Kae1, and Pcc1 hetero-pentamer protein complex (Zhang et al. 2015 ). Interestingly, this complex is universally conserved among Archaea and Eukarya, despite being absent in bacteria (Daugeron et al. 2011 ). Differently from the archaeal counterpart, eukaryotic KEOPS adopt a linear arrangement in its five protein components (Zhang et al. 2015 ). Cgi121 works in a genetic pathway and interacts with Bud32 (Bianchi & Shore, 2006 ). Telomeres are regions placed at the end of chromosomes composed of repetitive nucleotide sequences and specialized proteins. They organize chromosome replication and are involved in the recruitment of telomeres (Bianchi & Shore, 2006 ), thereby providing the essential cellular chromosome-end protection, and preserving telomere homeostasis (Daugeron et al. 2011 ). Specifically, the deletion of Cgi121, or other KEOPS components, leads to short telomeres. This implies the failure to add telomeres de novo to DNA double-strand breaks. Physiologically, KEOPS complex, moreover, promotes both telomere uncapping ad telomere elongation (Bianchi & Shore, 2006 ). Cgi121 and Bud32 form a protein complex with ADP that binds to the catalytic site of Bud32. This bond is arranged in the typical manner of the Protein Kinase A (PKA) protein family (Zhang et al. 2015 ). KEOPS is moreover required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t637A) in all tRNAs that read ANN codons (Wan et al. 2016 ). Nevertheless, Cgi121 is not required for tRNA modification.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M V V S I I P Q F P D I K V S L A L F E Q V K N A K E I R S K M S E L S T S F A F I D P R L V C S G E Q M Y S A I Y K T L I E V K Y N K M R T R N L N S E C V L C L S P T S N I S D A F L K F G I K D D S S Q L I C L K F H T N T D D V D K E Q L R T I M T S I V K G Q E I E F N D D N L S R F Y D E A L I R K I Y K L S D D F K P Q D V N G L S R A L V D A I Q L R G V
20406080100120140160180MVVSIIPQFPDIKVSLALFEQVKNAKEIRSKMSELSTSFAFIDPRLVCSGEQMYSAIYKTLIEVKYNKMRTRNLNSECVLCLSPTSNISDAFLKFGIKDDSSQLICLKFHTNTDDVDKEQLRTIMTSIVKGQEIEFNDDNLSRFYDEALIRKIYKLSDDFKPQDVNGLSRALVDAIQLRGVSequenceGHTBSN

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-Q03705-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q03705-F1.cif  
DSSP Secondary Structures   Q03705.dssp  





Publications:

Links:

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