ISDA

Deposition Date 2022-10-04

Release Date 2023-04-05

Last Version Date 2024-02-07

Entry Detail

PDB ID:

8B8H

Keywords:

ISOMERASE

Title:

Structure of DCS-resistant variant D322N of alanine racemase from M. tuberculosis in complex with DCS

Biological Source:

Source Organism:

Mycobacterium tuberculosis H37Rv (Taxon ID: 83332)

Host Organism:

Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.78 Å

R-Value Free:

0.22

R-Value Work:

0.19

R-Value Observed:

0.20

Space Group:

P 41 21 2

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Alanine racemase
Gene (Uniprot):alr
Mutations:D322N
Chain IDs:A, B
Chain Length:387
Number of Molecules:2
Biological Source:Mycobacterium tuberculosis H37Rv

UniProt ID:P9WQA9 Pfam ID:PF01168, PF00842 EC:5.1.1.1

Ligand Molecules

EDO

GOL

L7N

OJQ

Primary Citation

Structure of the d-Cycloserine-Resistant Variant D322N of Alanine Racemase from Mycobacterium tuberculosis .

de Chiara, C, Prosser, G.A, Ogrodowicz, R, de Carvalho, L.P.S, Evangelopoulos, D, Prosser, G.A, Rodgers, A, Dagg, B.M, Khatri, B, Ho, M.M, Gutierrez, M.G, Cortes, T, de Carvalho, L.P.S, de Chiara, C, Homsak, M, Prosser, G.A, Douglas, H.L, Garza-Garcia, A, Kelly, G, Purkiss, A.G, Tate, E.W, de Carvalho, L.P.S, Afonine, P.V, Grosse-Kunstleve, R.W, Echols, N, Headd, J.J, Moriarty, N.W, Mustyakimov, M, Terwilliger, T.C, Urzhumtsev, A, Zwart, P.H, Adams, P.D, Liebschner, D, Afonine, P.V, Baker, M.L, Bunkoczi, G, Chen, V.B, Croll, T.I, Hintze, B, Hung, L.W, Jain, S, McCoy, A.J, Moriarty, N.W, Oeffner, R.D, Poon, B.K, Prisant, M.G, Read, R.J, Richardson, J.S, Richardson, D.C, Sammito, M.D, Sobolev, O.V, Stockwell, D.H, Terwilliger, T.C, Urzhumtsev, A.G, Videau, L.L, Williams, C.J, Adams, P.D.Show

Acs Bio Med Chem Au 3 233 239 (2023)

PMID: 37363078 DOI: 10.1021/acsbiomedchemau.2c00074

Abstact

Alanine racemase (Alr) is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the racemization of l-alanine to d-alanine. Alr is one of the two targets of the broad-spectrum antibiotic d-cycloserine (DCS), a structural analogue of d-alanine. Despite being an essential component of regimens used to treat multi- and extensively drug-resistant tuberculosis for almost seven decades, resistance to DCS has not been observed in patients. We previously demonstrated that DCS evades resistance due to an ultralow rate of emergence of mutations. Yet, we identified a single polymorphism (converting Asp322 to Asn) in the alr gene, which arose in 8 out of 11 independent variants identified and that confers resistance. Here, we present the crystal structure of the Alr variant D322N in both the free and DCS-inactivated forms and the characterization of its DCS inactivation mechanism by UV-visible and fluorescence spectroscopy. Comparison of these results with those obtained with wild-type Alr reveals the structural basis of the 240-fold reduced inhibition observed in Alr D322N.

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