6X91 | pdb_00006x91

Crystal structure of MBP-fused human APOBEC1

PDB DOI: https://doi.org/10.2210/pdb6X91/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli, Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-06-02 Released: 2020-12-09
Deposition Author(s): Wolfe, A.D., Li, S.-X., Chen, X.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.51 Å
R-Value Free:
0.298 (Depositor), 0.295 (DCC)
R-Value Work:
0.276 (Depositor), 0.277 (DCC)
R-Value Observed:
0.278 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The structure of APOBEC1 and insights into its RNA and DNA substrate selectivity.

Wolfe, A.D., Li, S., Goedderz, C., Chen, X.S.

(2020) NAR Cancer 2: zcaa027-zcaa027

PubMed: 33094286 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/narcan/zcaa027
Primary Citation Related Structures:
6X91

PubMed Abstract:
APOBEC1 (APO1), a member of AID/APOBEC nucleic acid cytosine deaminase family, can edit apolipoprotein B mRNA to regulate cholesterol metabolism. This APO1 RNA editing activity requires a cellular cofactor to achieve tight regulation. However, no cofactors are required for deamination on DNA by APO1 and other AID/APOBEC members, and aberrant deamination on genomic DNA by AID/APOBEC deaminases has been linked to cancer. Here, we present the crystal structure of APO1, which reveals a typical APOBEC deaminase core structure, plus a unique well-folded C-terminal domain that is highly hydrophobic. This APO1 C-terminal hydrophobic domain (A1HD) interacts to form a stable dimer mainly through hydrophobic interactions within the dimer interface to create a four-stranded β-sheet positively charged surface. Structure-guided mutagenesis within this and other regions of APO1 clarified the importance of the A1HD in directing RNA and cofactor interactions, providing insights into the structural basis of selectivity on DNA or RNA substrates.

Organizational Affiliation

Genetics, Molecular and Cellular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.

Macromolecule Content

Total Structure Weight: 543 kDa
Atom Count: 37,624
Modeled Residue Count: 4,667
Deposited Residue Count: 4,744
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera	A, B, C, D, E A, B, C, D, E, F, G, H	593	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 9 Gene Names: DAH37_23060, APOBEC1 EC: 3.5.4.36 (PDB Primary Data), 3.5.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9 Go to UniProtKB: P0AEX9
Find proteins for P41238 (Homo sapiens) Explore P41238 Go to UniProtKB: P41238
PHAROS: P41238 GTEx: ENSG00000111701
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P41238 P0AEX9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	I, J, K, L, M I, J, K, L, M, N, O, P, Q, R, S, T, U, V	2		N/A	Interactions Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Interactions & Density Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC Query on CAC Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain DA [auth D] SDF format, chain FA [auth E] SDF format, chain HA [auth F] SDF format, chain JA [auth G] SDF format, chain LA [auth H] SDF format, chain X [auth A] SDF format, chain Z [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain LA [auth H] mmCIF format, chain X [auth A] mmCIF format, chain Z [auth B]	BA [auth C] DA [auth D] FA [auth E] HA [auth F] JA [auth G] BA [auth C], DA [auth D], FA [auth E], HA [auth F], JA [auth G], LA [auth H], X [auth A], Z [auth B]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain BA [auth C] Focus chain DA [auth D] Focus chain FA [auth E] Focus chain HA [auth F] Focus chain JA [auth G] Focus chain LA [auth H] Focus chain X [auth A] Focus chain Z [auth B] Interactions & Density Focus chain BA [auth C] Focus chain DA [auth D] Focus chain FA [auth E] Focus chain HA [auth F] Focus chain JA [auth G] Focus chain LA [auth H] Focus chain X [auth A] Focus chain Z [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain W [auth A] SDF format, chain KA [auth H] SDF format, chain IA [auth G] SDF format, chain GA [auth F] SDF format, chain EA [auth E] SDF format, chain CA [auth D] SDF format, chain AA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain W [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain IA [auth G] MOL2 format, chain GA [auth F] MOL2 format, chain EA [auth E] MOL2 format, chain CA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain W [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain IA [auth G] mmCIF format, chain GA [auth F] mmCIF format, chain EA [auth E] mmCIF format, chain CA [auth D] mmCIF format, chain AA [auth C]	AA [auth C] CA [auth D] EA [auth E] GA [auth F] IA [auth G] AA [auth C], CA [auth D], EA [auth E], GA [auth F], IA [auth G], KA [auth H], W [auth A], Y [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain CA [auth D] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain KA [auth H] Focus chain W [auth A] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth C] Focus chain CA [auth D] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain KA [auth H] Focus chain W [auth A] Focus chain Y [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001 Query on PRD_900001	I, J, K, L, M I, J, K, L, M, N, O, P, Q, R, S, T, U, V	alpha-maltose	Oligosaccharide / Nutrient		Interactions Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Interactions & Density Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V