8JEM

DltB tetramer in complex with inhibitor m-AMSA

PDB DOI: https://doi.org/10.2210/pdb8JEM/pdb
EM Map EMD-36192: EMDB EMDataResource

Classification: MEMBRANE PROTEIN/INHIBITOR
Organism(s): Streptococcus thermophilus LMG 18311
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2023-05-16 Released: 2024-05-15
Deposition Author(s): Zhang, P., Liu, Z.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.23 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 8JES 8JF2

Literature

Structural insights into the transporting and catalyzing mechanism of DltB in LTA D-alanylation.

Zhang, P., Liu, Z.

(2024) Nat Commun 15: 3404-3404

PubMed: 38649359 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-024-47783-7
Primary Citation of Related Structures:
8JEM, 8JES, 8JF2

PubMed Abstract:
DltB, a model member of the Membrane-Bound O-AcylTransferase (MBOAT) superfamily, plays a crucial role in D-alanylation of the lipoteichoic acid (LTA), a significant component of the cell wall of gram-positive bacteria. This process stabilizes the cell wall structure, influences bacterial virulence, and modulates the host immune response. Despite its significance, the role of DltB is not well understood. Through biochemical analysis and cryo-EM imaging, we discover that Streptococcus thermophilus DltB forms a homo-tetramer on the cell membrane. We further visualize DltB in an apo form, in complex with DltC, and in complex with its inhibitor amsacrine (m-AMSA). Each tetramer features a central hole. The C-tunnel of each protomer faces the intratetramer interface and provides access to the periphery membrane. Each protomer binds a DltC without changing the tetrameric organization. A phosphatidylglycerol (PG) molecule in the substrate-binding site may serve as an LTA carrier. The inhibitor m-AMSA bound to the L-tunnel of each protomer blocks the active site. The tetrameric organization of DltB provides a scaffold for catalyzing D-alanyl transfer and regulating the channel opening and closing. Our findings unveil DltB's dual function in the D-alanylation pathway, and provide insight for targeting DltB as a anti-virulence antibiotic.

Organizational Affiliation

Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China. pingfeng.zhang@whu.edu.cn.

Macromolecule Content

Total Structure Weight: 236.38 kDa
Atom Count: 15,930
Modelled Residue Count: 1,674
Deposited Residue Count: 1,760
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Teichoic acid D-alanyltransferase	A, B, C, D	440	Streptococcus thermophilus LMG 18311	Mutation(s): 0 Gene Names: dltB, stu0762 EC: 2.3.1 Membrane Entity: Yes
UniProt
Find proteins for Q5M4V4 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M4V4 Go to UniProtKB: Q5M4V4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5M4V4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGT (Subject of Investigation/LOI) Query on PGT Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain PA [auth C] SDF format, chain WA [auth D] SDF format, chain F [auth A] SDF format, chain GA [auth C] SDF format, chain Q [auth B] SDF format, chain RA [auth D] SDF format, chain U [auth B] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain WA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain U [auth B]	F [auth A] GA [auth C] O [auth A] PA [auth C] Q [auth B] F [auth A], GA [auth C], O [auth A], PA [auth C], Q [auth B], RA [auth D], U [auth B], WA [auth D]	(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE C₄₀ H₇₉ O₁₀ P KBPVYRBBONZJHF-AMAPPZPBSA-N		Interactions Focus chain F [auth A] Focus chain GA [auth C] Focus chain O [auth A] Focus chain PA [auth C] Focus chain Q [auth B] Focus chain RA [auth D] Focus chain U [auth B] Focus chain WA [auth D] Interactions & Density Focus chain F [auth A] Focus chain GA [auth C] Focus chain O [auth A] Focus chain PA [auth C] Focus chain Q [auth B] Focus chain RA [auth D] Focus chain U [auth B] Focus chain WA [auth D]
DGA (Subject of Investigation/LOI) Query on DGA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain JA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain JA [auth C]	H [auth A], JA [auth C]	DIACYL GLYCEROL C₃₉ H₇₆ O₅ UHUSDOQQWJGJQS-QNGWXLTQSA-N		Interactions Focus chain H [auth A] Focus chain JA [auth C] Interactions & Density Focus chain H [auth A] Focus chain JA [auth C]
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain FB [auth D] SDF format, chain HA [auth C] SDF format, chain NA [auth C] SDF format, chain UA [auth D] SDF format, chain AA [auth B] SDF format, chain AB [auth D] SDF format, chain BA [auth B] SDF format, chain BB [auth D] SDF format, chain CA [auth B] SDF format, chain CB [auth D] SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain EA [auth B] SDF format, chain EB [auth D] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain OA [auth C] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain SA [auth D] SDF format, chain T [auth B] SDF format, chain TA [auth D] SDF format, chain V [auth B] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain HA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain UA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D]	AA [auth B] AB [auth D] BA [auth B] BB [auth D] CA [auth B] AA [auth B], AB [auth D], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], EA [auth B], EB [auth D], FB [auth D], G [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], OA [auth C], R [auth B], S [auth B], SA [auth D], T [auth B], TA [auth D], UA [auth D], V [auth B], VA [auth D], W [auth B], X [auth B], XA [auth D], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain G [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain G [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
ASW (Subject of Investigation/LOI) Query on ASW Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain FA [auth C] SDF format, chain P [auth B] SDF format, chain QA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth D]	E [auth A], FA [auth C], P [auth B], QA [auth D]	N-[4-(acridin-9-ylamino)-3-methoxyphenyl]methanesulfonamide C₂₁ H₁₉ N₃ O₃ S XCPGHVQEEXUHNC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain FA [auth C] Focus chain P [auth B] Focus chain QA [auth D] Interactions & Density Focus chain E [auth A] Focus chain FA [auth C] Focus chain P [auth B] Focus chain QA [auth D]