Journal of Molecular Biology
Regular articleDetermination of the MurD mechanism through crystallographic analysis of enzyme complexes1
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Cited by (137)
The crystal structure of Mycobacterium thermoresistibile MurE ligase reveals the binding mode of the substrate m-diaminopimelate
2023, Journal of Structural BiologyRecent developments on UDP-N-acetylmuramoyl-L-alanine-D-gutamate ligase (Mur D) enzyme for antimicrobial drug development: An emphasis on in-silico approaches
2022, Current Research in Pharmacology and Drug DiscoveryCitation Excerpt :These divalent cations are not required for the binding of the substrates UMA and ADP, but play a crucial role in the ligase action of the MurD enzyme (Kotnik et al., 2007). The principle residues of the MurD enzyme of E. coli which take part while interacting with the substrate UMA involves amino acid residues Leu15, Thr16, Asp35, Thr36, Arg37, Gly73, and Asn138, while His183 interacts with Mg2+(Bertrand et al., 1997, 1999, 2000; Bertrand et al., 1999). At the same time, ADP interacts with Gly114, Lys115, Ser116, Thr117, Asn271, Arg302, and Asp317 residues.
The Mur Enzymes Chink in the Armour of Mycobacterium tuberculosis cell wall
2021, European Journal of Medicinal ChemistryConformational dynamics of a multidomain protein by neutron scattering and computational analysis
2021, Biophysical JournalCitation Excerpt :A MurD has 437 amino acid residues and consists of three domains, which are defined as from 1 to 93 (D1), 94–298 (D2), and 299–437 (D3) in the amino acid sequence (29). So far, numerous crystal structures of MurD have been identified (29–31), including the apo state (Protein Data Bank (PDB): 1E0E (29)), intermediate states (PDB: 5A5E and 5A5F (32)), and compound 1 (N-({3-[({4-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl}amino)methyl]phenyl}carbonyl)-D-glutamic acid) inhibitor-bound state (PDB: 2X5O (33)). These crystal structures are shown in Fig. 1 and suggest that one of the three domains of MurD, i.e., domain 3 (D3), undergoes drastic conformational change from the open form to the closed one via the semiclosed one upon ligand bindings, which is relevant to the enzymatic function (12,28–33).
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Edited by R. Huber