Modomics - A Database of RNA Modifications

ID Card:

Full name: 140 kDa actin-binding protein
Synonym: Abp140
GI: 398365899
COG: COG2226
UniProt: Q08641
Structures: | 7AD9 | 7BTE |
Alpha Fold Predicted Structure: AF-Q08641-F1
Enzyme type: methyltransferase
Position of modification - modification: t:32 - m3C


PDB Structures:


7AD9

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Lifeact is a short actin-binding peptide that is used to visualize filamentous actin (F-actin) structures in live eukaryotic cells using fluorescence microscopy. However, this popular probe has been shown to alter cellular morphology by affecting the structure of the cytoskeleton. The molecular basis for such artefacts is poorly understood. Here, we determined the high-resolution structure of the Lifeact-F-actin complex using electron cryo-microscopy (cryo-EM). The structure reveals that Lifeact interacts with a hydrophobic binding pocket on F-actin and stretches over 2 adjacent actin subunits, stabilizing the DNase I-binding loop (D-loop) of actin in the closed conformation. Interestingly, the hydrophobic binding site is also used by actin-binding proteins, such as cofilin and myosin and actin-binding toxins, such as the hypervariable region of TccC3 (TccC3HVR) from Photorhabdus luminescens and ExoY from Pseudomonas aeruginosa. In vitro binding assays and activity measurements demonstrate that Lifeact indeed competes with these proteins, providing an explanation for the altering effects of Lifeact on cell morphology in vivo. Finally, we demonstrate that the affinity of Lifeact to F-actin can be increased by introducing mutations into the peptide, laying the foundation for designing improved actin probes for live cell imaging.

Download RCSB-PDB Structures:

Pdb Files   7AD9.pdb   7BTE.pdb  
Pdbx/mmCIF Files   7AD9.cif   7BTE.cif  


Protein sequence:

MGVADLIKKFESISKEEGDATVDTNSSSKPLKSNDETKELHQQESTAVPQEVDVNEEFENEPETINSSRTAEKPLETNLPKPETNEEDEEEGSMSENKIYSKGENADINVNDFQEYKEMENTGAEVLASSVEESDAIQEGVAEETEGIATPKQKENEKNDESEEESANNASEPAEEYSQSEEDADIEQSNGKETENAENASQQANDGSTSTTTSKNKKKKNKKKNKKKRNGNVNTNANVDDSTKTGENDDTTGDTTSSTTSAIQEVNDLEVVDDSCLGIDQQHNREHLKALTQDVKEETLENIAHEGRGDNTGDQNAVEKSDFEKSDTEGSRIGRDLPFEFGKRNLTEESDVWDHNAWDNVEWGEEQVQQAEEKIKEQFKHPVPEFDKKLYNENPARYWDIFYKNNKENFFKDRKWLQIEFPILYASTRKDAEPVTIFEIGCGAGNTFFPILKDNENENLRIIAADFAPRAVELVKNSEQFNPKYGHATVWDLANPDGNLPDGVEPHSVDIAVMIFVFSALAPNQWDQAMDNLHKILKPGGKIIFRDYGAYDLTQVRFKKNRILEENFYVRGDGTRVYFFSEEKLREIFTKKYFLENKIGTDRRLLVNRKRQLKMYRCWVQAVFDVPQ

Comments:

Primer extension experiment shown that this enzyme is responsible for m3C modification in position 32 in all Ser and Thr tRNAs. The activity was tested in vitro on tRNAThrIGU. AdoMet is the methyl group donor.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
C:m3C tRNA (t) Thr/IGU/eukaryotic cytosol 32 IGU IGU tRNAThrIGU anticodon-loop Cytoplasm 21518805    21518804   
C:m3C RNA tRNA 32 IGA IGA tRNASerIGA anticodon-loop Cytoplasm 21518805    21518804   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q08641-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q08641-F1.cif  
DSSP Secondary Structures   Q08641.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae. Noma A, Yi S, Katoh T, Takai Y, Suzuki T, Suzuki T RNA [details] 21518805 -
A domain of the actin binding protein Abp140 is the yeast methyltransferase responsible for 3-methylcytidine modification in the tRNA anti-codon loop. D'Silva S, Haider SJ, Phizicky EM RNA [details] 21518804 -

Links:

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