9L8H

The structure of HitB-HitD complex with a C4 pantetheine cross-linking probe

This is a non-PDB format compatible entry.

Summary for 9L8H

• Entry DOI: 10.2210/pdb9l8h/pdb
• Descriptor: Putative ATP-dependent b-aminoacyl-ACP synthetase, Putative ACP, ADENOSINE-5'-DIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: hitachimycin, polyketide biosynthesis, carrier protein, adenylation, atp binding, ligase
• Biological source: Embleya scabrispora; More
• Total number of polymer chains: 2
• Total formula weight: 71674.87

Authors

Miyanaga, A.,Nagata, K.,Chisuga, T.,Kudo, F.,Eguchi, T. (deposition date: 2024-12-27, release date: 2026-01-21, Last modification date: 2026-04-29)

Primary citation

Arata, I.,Nagata, K.,Miyoshi, H.,Ishikawa, F.,Chisuga, T.,Kashima, T.,Tanabe, G.,Kudo, F.,Eguchi, T.,Fushinobu, S.,Miyanaga, A.
Investigation of the Linker-Length Preferences of Pantetheine Probes in the Cross-Linking Reactions Between Adenylation Enzymes and Carrier Proteins.
Chembiochem, 27:e70359-e70359, 2026

PubMed Abstract: Adenylation enzymes transfer acyl substrates selectively onto carrier proteins (CPs) in natural product biosynthesis. Despite the importance of adenylation enzyme-CP interactions, structural information on these transient complexes remains limited. Previously, we developed a pantetheine cross-linking probe (named C2Br), which contains an ethylenediamine linker with a reactive bromoacetamide group, and determined the structure of the cross-linked complex of the adenylation enzyme HitB with the CP HitD. Here, we investigated the linker-length effects of pantetheine probes in the cross-linking reactions of two adenylation enzymes, HitB and EntE, with CPs using probes with different diamine linkers, such as C2Br and C4Br, the latter containing a longer butanediamine linker moiety. Both adenylation enzymes formed cross-linked complexes with CPs irrespective of the probe used, but the reaction efficiencies depended on the linker length. Crystal structural analysis showed that the HitB-HitD interface interactions in the HitB-C4Br-HitD complex are essentially identical to those in the HitB-C2Br-HitD complex. In contrast, the diamine moieties of probes adopt different interaction modes, accounting for the observed variations in cross-linking efficiencies. A repertoire of pantetheine probes with varying linker lengths will facilitate structural studies on adenylation enzyme-CP interactions by enabling optimization for each adenylation enzyme.

PubMed: 42011964
DOI: 10.1002/cbic.70359

Experimental method

X-RAY DIFFRACTION (1.85 Å)