6K3K

Solution structure of APOBEC3G-CD2 with ssDNA, Product B


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Investigations on the Interactions between Cytidine Deaminase Human APOBEC3G and DNA.

Yan, X.Lan, W.Wang, C.Cao, C.

(2019) Chem Asian J 14: 2235-2241

  • DOI: 10.1002/asia.201900480
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human APOBEC3G (A3G) is a cytidine deaminase, which inhibits the replication of human immunodeficiency virus-1 by deaminating cytidine at 3'-end in target motif 5'-CCCA-3' in viral cDNA during the reverse transcription. It can in vitro deaminate two ...

    Human APOBEC3G (A3G) is a cytidine deaminase, which inhibits the replication of human immunodeficiency virus-1 by deaminating cytidine at 3'-end in target motif 5'-CCCA-3' in viral cDNA during the reverse transcription. It can in vitro deaminate two consecutive cytidines in a 3'->5' order. Although the crystal structure of A3G catalytic domain (A3G-CD2) variant with DNA was reported, it's still unknown why the residues involved in DNA binding and enzymatic deamination are distributed widely on its surface. To address this, we introduced steric iodine into C-5 position of cytidine (dC6I) in substrate 5'-ATTC4C5C6IA7ATT-3' DNA (abbreviated as TCCC6I). This modification significantly switches the sequence preference of A3G catalytic deamination from 5'-CCC-3' into 5'-TCC-3', although slight dC6I deamination was observed. Solution structures of A3G-CD2 in complex with deamination products TCUC6I DNA and TCUU6I DNA were resolved, which indicate that substrate DNA interacts with A3G-CD2 in two binding modes (termed as TCC and CCC). The dC6 deamination rate is dependent on the type of the most 5'-end base in the motif 5'-XCCA-3' (X=C,T,A or G). CCC mode is in favour of dC6 deamination, while TCC mode avails dC5 deamination. These studies present extensively structural basis to design inhibitors to impede the evolvability of viruses.


    Organizational Affiliation

    Shanghai Institute of Organic Chmeistry, Chinese Academy of Sciences, State Key Laboratory of Natural Products and Bio-organic Chemistry, 345 Lingling Road, 200032, Shanghai, CHINA.,CHINA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA dC->dU-editing enzyme APOBEC-3G
A
188Homo sapiensMutation(s): 0 
Gene Names: APOBEC3G
EC: 3.5.4.-
Find proteins for Q9HC16 (Homo sapiens)
Go to Gene View: APOBEC3G
Go to UniProtKB:  Q9HC16
Entity ID: 2
MoleculeChainsLengthOrganism
DNA/RNA (5'-D(*AP*TP*TP*CP*UP*(ICY)P*AP*AP*TP*T)-3')B10synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
C38
Query on C38
B
DNA LINKINGC9 H13 I N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China21778065

Revision History 

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-07-17
    Type: Data collection, Database references