Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22153.40 
• Atom Count: 1524 
• Residue Count: 189 
• Unique protein chains: 1

3E1U

The Crystal Structure of the Anti-Viral APOBEC3G Catalytic Domain

• DOI: 10.2210/pdb3E1U/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2008-08-04 Released: 2008-10-07 
• Deposition Author(s): Holden, L., Prochnow, C., Chang, Y.P., Bransteitter, R., Chelico, L., Sen, U., Stevens, R.C., Goodman, R.F., Chen, X.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.267 
• R-Value Work: 0.251 

Literature

Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications.

Holden, L.G., Prochnow, C., Chang, Y.P., Bransteitter, R., Chelico, L., Sen, U., Stevens, R.C., Goodman, M.F., Chen, X.S.

(2008) Nature 456: 121-124

• PubMed: 18849968 
• DOI: 10.1038/nature07357
• Primary Citation of Related Structures:  
  3IQS


• PubMed Abstract: 
  

The APOBEC family members are involved in diverse biological functions. APOBEC3G restricts the replication of human immunodeficiency virus (HIV), hepatitis B virus and retroelements by cytidine deamination on single-stranded DNA or by RNA binding. Here we report the high-resolution crystal structure of the carboxy-terminal deaminase domain of APOBEC3G (APOBEC3G-CD2) purified from Escherichia coli. The APOBEC3G-CD2 structure has a five-stranded beta-sheet core that is common to all known deaminase structures and closely resembles the structure of another APOBEC protein, APOBEC2 (ref. 5). A comparison of APOBEC3G-CD2 with other deaminase structures shows a structural conservation of the active-site loops that are directly involved in substrate binding. In the X-ray structure, these APOBEC3G active-site loops form a continuous 'substrate groove' around the active centre. The orientation of this putative substrate groove differs markedly (by 90 degrees) from the groove predicted by the NMR structure. We have introduced mutations around the groove, and have identified residues involved in substrate specificity, single-stranded DNA binding and deaminase activity. These results provide a basis for understanding the underlying mechanisms of substrate specificity for the APOBEC family.

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Organizational Affiliation: 

Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA dC->dU-editing enzyme APOBEC-3G	A	189	Homo sapiens	Mutation(s): 0  Gene Names: APOBEC3G EC: 3.5.4.-
Find proteins for Q9HC16 (Homo sapiens) Go to Gene View: APOBEC3G Go to UniProtKB:  Q9HC16

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.267 
• R-Value Work: 0.251 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 83.464	α = 90.00
b = 57.329	β = 96.46
c = 40.578	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data scaling
HKL-2000	data reduction
CNS	refinement
SHARP	phasing
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-08-04 
• Released Date: 2008-10-07 
• Deposition Author(s): Holden, L., Prochnow, C., Chang, Y.P., Bransteitter, R., Chelico, L., Sen, U., Stevens, R.C., Goodman, R.F., Chen, X.S.

Revision History 

• Version 1.0: 2008-10-07
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance