Modomics - A Database of RNA Modifications

ID Card:

Full name: DNA dC->dU-editing enzyme APOBEC-3B
GI: 12643884
UniProt: Q9UH17
Structures: | 2NBQ | 5CQD | 5CQH | 5CQI | 5CQK | 5SXG | 5SXH | 5TD5 | 5TKM | 5NFK | 6NFL | 6NFM | 7RW6 |
Alpha Fold Predicted Structure: AF-Q9UH17-F1
Enzyme type: deaminase


PDB Structures:


2NBQ

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Human APOBEC3B (A3B) is a member of the APOBEC3 (A3) family of cytidine deaminases, which function as DNA mutators and restrict viral pathogens and endogenous retrotransposons. Recently, A3B was identified as a major source of genetic heterogeneity in several human cancers. Here, we determined the solution nuclear magnetic resonance structure of the catalytically active C-terminal domain (CTD) of A3B and performed detailed analyses of its deaminase activity. The core of the structure comprises a central five-stranded β-sheet with six surrounding helices, common to all A3 proteins. The structural fold is most similar to that of A3A and A3G-CTD, with the most prominent difference being found in loop 1. The catalytic activity of A3B-CTD is ∼15-fold lower than that of A3A, although both exhibit a similar pH dependence. Interestingly, A3B-CTD with an A3A loop 1 substitution had significantly increased deaminase activity, while a single-residue change (H29R) in A3A loop 1 reduced A3A activity to the level seen with A3B-CTD. This establishes that loop 1 plays an important role in A3-catalyzed deamination by precisely positioning the deamination-targeted C into the active site. Overall, our data provide important insights into the determinants of the activities of individual A3 proteins and facilitate understanding of their biological function.

Download RCSB-PDB Structures:

Pdb Files   2NBQ.pdb   5CQD.pdb   5CQH.pdb   5CQI.pdb   5CQK.pdb   5NFK.pdb   5SXG.pdb   5SXH.pdb   5TD5.pdb   5TKM.pdb   6NFL.pdb   6NFM.pdb   7RW6.pdb  
Pdbx/mmCIF Files   2NBQ.cif   5CQD.cif   5CQH.cif   5CQI.cif   5CQK.cif   5NFK.cif   5SXG.cif   5SXH.cif   5TD5.cif   5TKM.cif   6NFL.cif   6NFM.cif   7RW6.cif  


Protein sequence:

MNPQIRNPMERMYRDTFYDNFENEPILYGRSYTWLCYEVKIKRGRSNLLWDTGVFRGQVYFKPQYHAEMCFLSWFCGNQLPAYKCFQITWFVSWTPCPDCVAKLAEFLSEHPNVTLTISAARLYYYWERDYRRALCRLSQAGARVTIMDYEEFAYCWENFVYNEGQQFMPWYKFDENYAFLHRTLKEILRYLMDPDTFTFNFNNDPLVLRRRQTYLCYEVERLDNGTWVLMDQHMGFLCNEAKNLLCGFYGRHAELRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFEYCWDTFVYRQGCPFQPWDGLEEHSQALSGRLRAILQNQGN

Comments:





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q9UH17-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q9UH17-F1.cif  
DSSP Secondary Structures   Q9UH17.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI