8D32 image
Entry Detail
PDB ID:
8D32
Keywords:
Title:
Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase bound to 5-deoxyadenosylrhodibalamin and PPPi
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2022-05-31
Release Date:
2023-05-10
Method Details:
Experimental Method:
Resolution:
1.85 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
H 3 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Corrinoid adenosyltransferase
Chain IDs:A
Chain Length:193
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
Primary Citation
A Noble Metal Substitution Leads to B 12 Cofactor Mimicry by a Rhodibalamin.
Biochemistry 63 1955 1962 (2024)
PMID: 39012171 DOI: 10.1021/acs.biochem.4c00216

Abstact

In mammals, cobalamin is an essential cofactor that is delivered by a multitude of chaperones in an elaborate trafficking pathway to two client enzymes, methionine synthase and methylmalonyl-CoA mutase (MMUT). Rhodibalamins, the rhodium analogs of cobalamins, have been described as antimetabolites due to their ability to inhibit bacterial growth. In this study, we have examined the reactivity of adenosylrhodibalamin (AdoRhbl) with two key human chaperones, MMACHC (also known as CblC) and adenosyltransferase (MMAB, also known as ATR), and with the human and Mycobacterium tuberculosis MMUT. We demonstrate that while AdoRhbl binds tightly to all four proteins, the Rh-carbon bond is resistant to homolytic (on MMAB and MMUT) as well as heterolytic (on MMACHC) rupture. On the other hand, MMAB catalyzes Rh-carbon bond formation, converting rhodi(I)balamin in the presence of ATP to AdoRhbl. We report the first crystal structure of a rhodibalamin (AdoRhbl) bound to a B12 protein, i.e., MMAB, in the presence of triphosphate, which shows a weakened but intact Rh-carbon bond. The structure provides insights into how MMAB cleaves the corresponding Co-carbon bond in a sacrificial homolytic reaction that purportedly functions as a cofactor sequestration strategy. Collectively, the study demonstrates that while the noble metal substitution of cobalt by rhodium sets up structural mimicry, it compromises chemistry, which could be exploited for targeting human and bacterial B12 chaperones and enzymes.

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