Structural and molecular dynamics of ammonia transport in Staphylococcus aureus NH3-dependent NAD synthetase

Sultana, Kazi Nasrin; Srivastava, Sandeep

doi:10.1016/j.ijbiomac.2022.01.138

Cited by 4 publications

(4 citation statements)

References 13 publications

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“…The tunnel residues are known from the literature 31 . (d) NH 4 + -tunnel (mesh representation) of bacterial NH 3 -NADS (PDB: 6kv3) The tunnel residues are known from the literature 36 . (e) P2 loop interacting with SDP residues 482 and 485.…”

Section: Analysis Of Nads Funfams and Their Function Determining Resi...mentioning

confidence: 99%

“…The NH 3 -NADS are single domain enzymes with no CN domain, thus they have no interdomain tunnels. However, they have been proposed to transport ammonia/ammonium ion (NH 4 + ) obtained from the environment from the binding site to the catalytic site, also via a tunnel 36 . Based on the molecular dynamics analysis by Sultana and Srivastava, this tunnel was deduced to be on the interface between two protomers of an NH 3 -NADS homodimer.…”

Section: Analysis Of Nads Funfams and Their Function Determining Resi...mentioning

confidence: 99%

“…Knowledge of structural motifs specific to bacterial GMPS/NADS FunFams could facilitate anti-bacterial drug development, as GMPS and NADS are essential enzymes involved in de novo purine synthesis 29 and the production of metabolic coenzyme NAD 30 , respectively. These enzymes represent potential targets for drug development against pathogenic microorganisms, such as Mycobacterium tuberculosis and Staphylococcus aureus 15,[31][32][33][34][35][36] . The ASSAM (Amino acid pattern Search for Substructures and Motifs) algorithm 37 allowed us to search these structural motifs against several protein structure databases including CATH and AlphaFold2, thus verifying the specificity and high conservation of the bacterial-FunFam-specific structural motifs.…”

Section: Substrate a + Atp → Substrate A-amp + Ppimentioning

confidence: 99%

“…* Some bacterial species have more than one domain copy and these paralogs are found in different FunFams -FunFam155 and FunFam106. ) obtained from the environment from the binding site to the catalytic site, also via a tunnel 36 . Based on the molecular dynamics analysis by Sultana and Srivastava, this tunnel was deduced to be on the interface between two protomers of an NH 3 -NADS homodimer.…”

Section: Different Multidomain Architectures Reflect Different Modes ...mentioning

confidence: 99%

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Understanding structural and functional diversity of ATP-PPases using protein domains and functional families in CATH database

Waman,

Yin,

Sen

et al. 2023

Preprint

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ATP-Pyrophosphatases (ATP-PPases) are the most primordial lineage of the large and diverse HUP (HIGH-motif proteins, Universal Stress Proteins, ATP-Pyrophosphatase) superfamily. There are four different ATP-PPase substrate-specificity groups, and members of each group show considerable sequence variation across the domains of life despite sharing the same catalytic function. Over the past decade, there has been a >20-fold expansion in the number of ATP-PPase domain structures most recently from advances in protein structure prediction (e.g. Alphafold2). Using the enriched structural information, we have characterised the two most populated ATP-PPase substrate-specificity groups, the NAD- synthases (NAD) and GMP synthases (GMPS). We performed local structural and sequence comparisons between the NADS and GMPS from different domains of life and identified taxonomic-group specific structural functional motifs. As GMPS and NADS are potential drug targets of pathogenic microorganisms including Mycobacterium tuberculosis, structural motifs specific to bacterial GMPS and NADS provide new insights that may aid antibacterial-drug design.

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Section: Analysis Of Nads Funfams and Their Function Determining Resi...mentioning

confidence: 99%

Section: Analysis Of Nads Funfams and Their Function Determining Resi...mentioning

confidence: 99%

Section: Substrate a + Atp → Substrate A-amp + Ppimentioning

confidence: 99%

Section: Different Multidomain Architectures Reflect Different Modes ...mentioning

confidence: 99%

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Understanding structural and functional diversity of ATP-PPases using protein domains and functional families in CATH database

Waman,

Yin,

Sen

et al. 2023

Preprint

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The multi-molecular mechanisms of tumor-targeted drug resistance in precision medicine

Huang

et al. 2022

Biomedicine & Pharmacotherapy

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Is BF.7 more infectious than other Omicron subtypes: Insights from structural and simulation studies of BF.7 spike RBD variant

Singh

Anand

Srivastava

2023

International Journal of Biological Macromolecules

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Structural and molecular dynamics of ammonia transport in Staphylococcus aureus NH3-dependent NAD synthetase

Cited by 4 publications

References 13 publications

Understanding structural and functional diversity of ATP-PPases using protein domains and functional families in CATH database

Understanding structural and functional diversity of ATP-PPases using protein domains and functional families in CATH database

The multi-molecular mechanisms of tumor-targeted drug resistance in precision medicine

Is BF.7 more infectious than other Omicron subtypes: Insights from structural and simulation studies of BF.7 spike RBD variant

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