5KDR | pdb_00005kdr

The crystal structure of carboxyltransferase from Staphylococcus Aureus bound to the antimicrobial agent moiramide B.

PDB DOI: https://doi.org/10.2210/pdb5KDR/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus USA300, Staphylococcus aureus RF122
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-06-08 Released: 2016-08-10
Deposition Author(s): Silvers, M.A., Pakhomova, S., Neau, D., Silvers, W.C., Anzalone, N., Taylor, C.M., Waldrop, G.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.276 (Depositor), 0.278 (DCC)
R-Value Work:
0.229 (Depositor), 0.233 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Carboxyltransferase from Staphylococcus aureus Bound to the Antibacterial Agent Moiramide B.

Silvers, M.A., Pakhomova, S., Neau, D.B., Silvers, W.C., Anzalone, N., Taylor, C.M., Waldrop, G.L.

(2016) Biochemistry 55: 4666-4674

PubMed: 27471863 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.biochem.6b00641
Primary Citation Related Structures:
5KDR

PubMed Abstract:
The dramatic increase in the prevalence of antibiotic-resistant bacteria has necessitated a search for new antibacterial agents against novel targets. Moiramide B is a natural product, broad-spectrum antibiotic that inhibits the carboxyltransferase component of acetyl-CoA carboxylase, which catalyzes the first committed step in fatty acid synthesis. Herein, we report the 2.6 Å resolution crystal structure of moiramide B bound to carboxyltransferase. An unanticipated but significant finding was that moiramide B bound as the enol/enolate. Crystallographic studies demonstrate that the (4S)-methyl succinimide moiety interacts with the oxyanion holes of the enzyme, supporting the notion that an anionic enolate is the active form of the antibacterial agent. Structure-activity studies demonstrate that the unsaturated fatty acid tail of moiramide B is needed only for entry into the bacterial cell. These results will allow the design of new antibacterial agents against the bacterial form of carboxyltransferase.

Organizational Affiliation

Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853-1301, United States.

Macromolecule Content

Total Structure Weight: 69.47 kDa
Atom Count: 4,338
Modeled Residue Count: 551
Deposited Residue Count: 612
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha	A	327	Staphylococcus aureus subsp. aureus USA300	Mutation(s): 0 Gene Names: accA, SAUSA300_1646 EC: 6.4.1.2 (PDB Primary Data), 2.1.3.15 (UniProt)
UniProt
Find proteins for Q2FXM7 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXM7 Go to UniProtKB: Q2FXM7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2FXM7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta	B	285	Staphylococcus aureus RF122	Mutation(s): 0 Gene Names: accD, SAB1559c EC: 6.4.1.2 (PDB Primary Data), 2.1.3.15 (UniProt)
UniProt
Find proteins for Q2FXM6 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXM6 Go to UniProtKB: Q2FXM6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2FXM6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YT5 Query on YT5 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	Moiramide B C₂₅ H₃₁ N₃ O₅ WMLLJSBRSSYYPT-PQUJRENYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.276 (Depositor), 0.278 (DCC)
R-Value Work: 0.229 (Depositor), 0.233 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.807	α = 90
b = 49.445	β = 91.94
c = 100.048	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-08-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-08-10
Type: Initial release
Version 1.1: 2016-08-24
Changes: Database references
Version 1.2: 2016-09-07
Changes: Database references
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary