8SBM

Crystal structure of the wild-type Catalytic ATP-binding domain of Mtb DosS

Summary for 8SBM

• Entry DOI: 10.2210/pdb8sbm/pdb
• Descriptor: GAF domain-containing protein, ZINC ION, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: doss, abd, transferase
• Biological source: Mycobacterium tuberculosis
• Total number of polymer chains: 2
• Total formula weight: 27250.55

Authors

Larson, G.,Shi, K.,Aihara, H.,Bhagi-Damodaran, A. (deposition date: 2023-04-03, release date: 2023-11-08, Last modification date: 2023-11-29)

Primary citation

Larson, G.W.,Windsor, P.K.,Smithwick, E.,Shi, K.,Aihara, H.,Rama Damodaran, A.,Bhagi-Damodaran, A.
Understanding ATP Binding to DosS Catalytic Domain with a Short ATP-Lid.
Biochemistry, 62:3283-3292, 2023

PubMed Abstract: DosS is a heme-containing histidine kinase that triggers dormancy transformation in. Sequence comparison of the catalytic ATP-binding (CA) domain of DosS to other well-studied histidine kinases reveals a short ATP-lid. This feature has been thought to block binding of ATP to DosS's CA domain in the absence of interactions with DosS's dimerization and histidine phospho-transfer (DHp) domain. Here, we use a combination of computational modeling, structural biology, and biophysical studies to re-examine ATP-binding modalities in DosS. We show that the closed-lid conformation observed in crystal structures of DosS CA is caused by the presence of Zn in the ATP binding pocket that coordinates with Glu537 on the ATP-lid. Furthermore, circular dichroism studies and comparisons of DosS CA's crystal structure with its AlphaFold model and homologous DesK reveal that residues 503-507 that appear as a random coil in the Zn-coordinated crystal structure are in fact part of the N-box α helix needed for efficient ATP binding. Such random-coil transformation of an N-box α helix turn and the closed-lid conformation are both artifacts arising from large millimolar Zn concentrations used in DosS CA crystallization buffers. In contrast, in the absence of Zn, the short ATP-lid of DosS CA has significant conformational flexibility and can effectively bind AMP-PNP ( = 53 ± 13 μM), a non-hydrolyzable ATP analog. Furthermore, the nucleotide affinity remains unchanged when CA is conjugated to the DHp domain ( = 51 ± 6 μM). In all, our findings reveal that the short ATP-lid of DosS CA does not hinder ATP binding and provide insights that extend to 2988 homologous bacterial proteins containing such ATP-lids.

PubMed: 37905955
DOI: 10.1021/acs.biochem.3c00306

Experimental method

X-RAY DIFFRACTION (1.47 Å)