8D32 | pdb_00008d32

Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase bound to 5-deoxyadenosylrhodibalamin and PPPi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.246 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.218 (Depositor) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

A Noble Metal Substitution Leads to B 12 Cofactor Mimicry by a Rhodibalamin.

Ruetz, M.Mascarenhas, R.Widner, F.Kieninger, C.Koutmos, M.Krautler, B.Banerjee, R.

(2024) Biochemistry 63: 1955-1962

  • DOI: https://doi.org/10.1021/acs.biochem.4c00216
  • Primary Citation Related Structures: 
    8D32

  • PubMed Abstract: 

    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 B 12 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 B 12 chaperones and enzymes.

Macromolecule Content 

  • Total Structure Weight: 22.65 kDa 
  • Atom Count: 1,558 
  • Modeled Residue Count: 186 
  • Deposited Residue Count: 193 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Corrinoid adenosyltransferase193Mycobacterium tuberculosisMutation(s): 0 
Gene Names: MT1354
EC: 2.5.1.17
UniProt
Find proteins for P9WP99 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WP99 
Go to UniProtKB:  P9WP99
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WP99
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF0
(Subject of Investigation/LOI)

Query on SF0



Download:Ideal Coordinates CCD File
B [auth A][5-(5,6-dimethyl-1H-benzimidazol-1-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl 1-{3-[3,14,19-tris(2-amino-2-oxoethyl)-8,13,18-tris(3-amino-3-oxopropyl)-1,4,6,9,9,14,16,19-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1~2,5~.1~7,10~.1~12,15~]tricosa-5(23),6,10,12(21),15,17(20)-hexaen-4-yl-kappa~4~N~20~,N~21~,N~22~,N~23~]propanamido}propan-2-yl hydrogenato phosphate]rhodium (non-preferred name)
C62 H89 N13 O14 P Rh
VWWNYPUYAVYGSM-SSEWGYSZSA-M
3PO
(Subject of Investigation/LOI)

Query on 3PO



Download:Ideal Coordinates CCD File
D [auth A]TRIPHOSPHATE
H5 O10 P3
UNXRWKVEANCORM-UHFFFAOYSA-N
5AD
(Subject of Investigation/LOI)

Query on 5AD



Download:Ideal Coordinates CCD File
C [auth A]5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.246 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.218 (Depositor) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.618α = 90
b = 62.618β = 90
c = 266.997γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesRO1-DK45776
American Heart AssociationUnited States19POST34370113

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Database references, Structure summary