3KZL|pdb_00003kzl

Crystal structure of BA2930 mutant (H183G) in complex with AcCoA

PDB DOI: https://doi.org/10.2210/pdb3KZL/pdb

Classification: TRANSFERASE
Organism(s): Bacillus anthracis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-12-08 Released: 2009-12-22
Deposition Author(s): Klimecka, M.M.,Chruszcz, M.,Porebski, P.J.,Cymborowski, M.,Anderson, W.F.,Minor, W.,Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.232 (Depositor), 0.190 (DCC)
R-Value Work:
0.180 (Depositor), 0.190 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structural Analysis of a Putative Aminoglycoside N-Acetyltransferase from Bacillus anthracis.

Klimecka, M.M., Chruszcz, M., Font, J., Skarina, T., Shumilin, I., Onopryienko, O., Porebski, P.J., Cymborowski, M., Zimmerman, M.D., Hasseman, J., Glomski, I.J., Lebioda, L., Savchenko, A., Edwards, A., Minor, W.

(2011) J Mol Biology 410: 411-423

PubMed: 21601576 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.jmb.2011.04.076
Primary Citation of Related Structures:
3E4F,3IJW,3KZL,3N0M,3N0S

PubMed Abstract:
For the last decade, worldwide efforts for the treatment of anthrax infection have focused on developing effective vaccines. Patients that are already infected are still treated traditionally using different types of standard antimicrobial agents. The most popular are antibiotics such as tetracyclines and fluoroquinolones. While aminoglycosides appear to be less effective antimicrobial agents than other antibiotics, synthetic aminoglycosides have been shown to act as potent inhibitors of anthrax lethal factor and may have potential application as antitoxins. Here, we present a structural analysis of the BA2930 protein, a putative aminoglycoside acetyltransferase, which may be a component of the bacterium's aminoglycoside resistance mechanism. The determined structures revealed details of a fold characteristic only for one other protein structure in the Protein Data Bank, namely, YokD from Bacillus subtilis. Both BA2930 and YokD are members of the Antibiotic_NAT superfamily (PF02522). Sequential and structural analyses showed that residues conserved throughout the Antibiotic_NAT superfamily are responsible for the binding of the cofactor acetyl coenzyme A. The interaction of BA2930 with cofactors was characterized by both crystallographic and binding studies.

Organizational Affiliation

Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.

Macromolecule Content

Total Structure Weight: 124.94 kDa
Atom Count: 8,859
Modelled Residue Count: 1,062
Deposited Residue Count: 1,072
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoglycoside N3-acetyltransferase	A, B [auth D], C, D [auth B]	268	Bacillus anthracis	Mutation(s): 1 Gene Names: aacC7, BA_2930, GBAA2930, GBAA_2930 EC: 2.3.1
UniProt
Find proteins for A0A3P1UCA6 (Bacillus anthracis) Explore A0A3P1UCA6 Go to UniProtKB: A0A3P1UCA6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3P1UCA6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO Query on ACO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth D] SDF format, chain L [auth C] SDF format, chain Q [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth D] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth D] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth B]	E [auth A], G [auth D], L [auth C], Q [auth B]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain E [auth A] Focus chain G [auth D] Focus chain L [auth C] Focus chain Q [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth D] Focus chain L [auth C] Focus chain Q [auth B]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain M [auth C] SDF format, chain U [auth B] SDF format, chain F [auth A] SDF format, chain H [auth D] SDF format, chain I [auth D] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain S [auth B] SDF format, chain V [auth B] MOL2 format, chain J [auth D] MOL2 format, chain M [auth C] MOL2 format, chain U [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth D] MOL2 format, chain I [auth D] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain S [auth B] MOL2 format, chain V [auth B] mmCIF format, chain J [auth D] mmCIF format, chain M [auth C] mmCIF format, chain U [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth D] mmCIF format, chain I [auth D] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain S [auth B] mmCIF format, chain V [auth B]	F [auth A] H [auth D] I [auth D] J [auth D] M [auth C] F [auth A], H [auth D], I [auth D], J [auth D], M [auth C], N [auth C], O [auth C], P [auth C], S [auth B], U [auth B], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth D] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth D] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth B] Focus chain U [auth B] Focus chain V [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain T [auth B] MOL2 format, chain K [auth D] MOL2 format, chain T [auth B] mmCIF format, chain K [auth D] mmCIF format, chain T [auth B]	K [auth D], T [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Focus chain T [auth B] Interactions & Density Focus chain K [auth D] Focus chain T [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B [auth D], C, D [auth B]	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.232 (Depositor), 0.190 (DCC)
R-Value Work: 0.180 (Depositor), 0.190 (DCC)
R-Value Observed: 0.183 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33KZL

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.831	α = 90
b = 109.182	β = 111.91
c = 73.721	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
SOLVE	phasing
RESOLVE	model building
ARP/wARP	model building
REFMAC	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing
RESOLVE	phasing