<scp>RCSB</scp> Protein Data Bank: Celebrating 50 years of the <scp>PDB</scp> with new tools for understanding and visualizing biological macromolecules in <scp>3D</scp>

Burley, S.K.; Bhikadiya, Charmi; Bi, Chunxiao; Bittrich, Sebastian; Chen, Li; Crichlow, G.V.; Duarte, José M.; Dutta, Shuchismita; Fayazi, Maryam; Feng, Zhang; Flatt, Justin W.; Ganesan, Sai J.; Goodsell, David S.; Ghosh, Sutapa; Green, Rachel Kramer; Guranovic, Vladimir; Henry, Jeremy; Hudson, Brian P.; Lawson, Catherine L.; Liang, Yu-He; Lowe, Robert; Peisach, Ezra; Persikova, Irina; Piehl, Dennis W.; Rose, Yana; Šali, Andrej; Segura, Joan; Sekharan, Monica; Shao, Chenghua; Vallat, Brinda; Voigt, Maria; Westbrook, John D.; Whetstone, Shamara; Young, Jasmine; Zardecki, Christine

doi:10.1002/pro.4213

Cited by 118 publications

(72 citation statements)

References 103 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The great advances for biocatalysts, which have already been achieved or can be developed in the future with breakthrough technologies, bring biocatalysts in a favorable position for the mild and selective removal of specific oxygen‐ and nitrogen‐containing functional groups. The unique classification system of the Enzyme Commission (EC Number) for enzymes according to the catalyzed reaction [207] as well as the use of databases and information/communication technologies for a growing number of characterized enzyme structures [208] and enzyme functions [209] provide a valuable scientific infrastructure.…”

Section: Discussionmentioning

confidence: 99%

Selective Biocatalytic Defunctionalization of Raw Materials

Wohlgemuth

2022

ChemSusChem

View full text Add to dashboard Cite

Biobased raw materials, such as carbohydrates, amino acids, nucleotides, or lipids contain valuable functional groups with oxygen and nitrogen atoms. An abundance of many functional groups of the same type, such as primary or secondary hydroxy groups in carbohydrates, however, limits the synthetic usefulness if similar reactivities cannot be differentiated. Therefore, selective defunctionalization of highly functionalized biobased starting materials to differentially functionalized compounds can provide a sustainable access to chiral synthons, even in case of products with fewer functional groups. Selective defunctionalization reactions, without affecting other functional groups of the same type, are of fundamental interest for biocatalytic reactions. Controlled biocatalytic defunctionalizations of biobased raw materials are attractive for obtaining valuable platform chemicals and building blocks. The biocatalytic removal of functional groups, an important feature of natural metabolic pathways, can also be utilized in a systemic strategy for sustainable metabolite synthesis.

show abstract

Section: Discussionmentioning

confidence: 99%

Selective Biocatalytic Defunctionalization of Raw Materials

Wohlgemuth

2022

ChemSusChem

View full text Add to dashboard Cite

show abstract

“…Firstly, we found the 2D structure of catechin on the PubChem website and transferred it to the 3D structure through ChemOffice software (version 2019, Cambridge Soft, Cambridge, MA, USA) with the optimization conditions of minimum free energy. Moreover, through the uniport database, we converted gene names to protein names which could be used to download their 3D structures on the Protein Data Bank (PDB) database [ 31 ]. Secondly, we deleted the water molecules and small molecule ligands, added hydrogen, and determined the active pocket in the protein 3D structure through Auto Dock Tools.…”

Section: Methodsmentioning

confidence: 99%

Catechin Mediates Ferroptosis to Exert an Anti-Inflammatory Effect on RAW 264.7 Cells

Kuang

Yang

Liu

et al. 2022

Foods

View full text Add to dashboard Cite

Catechin possesses a potential anti-inflammatory activity, but its anti-inflammatory mechanism is still unclear. Herein, the analysis of network pharmacology showed that catechin might mediate ferroptosis on macrophages to exhibit a significant anti-inflammatory effect on RAW264.7. The metabolomics further indicated that catechin might influence ferroptosis by activating two pathways of cysteine and methionine metabolism and glutathione metabolism, and inhibiting the pathway of ferroptosis to promote the reduction of l-methionine-s-oxide and s-glutathionyl-l-cysteine, and the reduction and synthesis of γ-glutamylcysteine. Furthermore, related proteins (MSRA, CDR, GSR and GCL) in three metabolic pathways and ferroptosis-related proteins (GPX4 and SLC7A11) might be relevant to catechin through molecular docking. Thus, we speculate that catechin plays an anti-inflammatory effect through mediating ferroptosis on RAW264.7, which still needs further focus on the detailed molecular mechanism.

show abstract

“…Structural-functional information is required for the rational engineering of UPOs to optimally catalyze selective hydroxylations and epoxidations of interest. Since the emergence of the first P450 crystal structures [10], many thousands of P450 entries have accumulated during the 50 years of history [11] of the Protein Data Bank (PDB, www.rcsb.org, accessed on 1 March 2022). In contrast, although Hofrichter and coworkers [12] reported (from BLAST search in November 2021) the presence of over 4000 putative UPO/HTP encoding genes in the NCBI database and over 8000 in the sequenced fungal genomes available at Mycocosm (JGI, DOE), only 19 PDB entries refer to UPO enzymes (including complexes with different ligands) and UPO structures from only two fungal species have been published to date.…”

Section: Introductionmentioning

confidence: 99%

Structural Characterization of Two Short Unspecific Peroxygenases: Two Different Dimeric Arrangements

et al. 2022

View full text Add to dashboard Cite

Unspecific peroxygenases (UPOs) are extracellular fungal enzymes of biotechnological interest as self-sufficient (and more stable) counterparts of cytochrome P450 monooxygenases, the latter being present in most living cells. Expression hosts and structural information are crucial for exploiting UPO diversity (over eight thousand UPO-type genes were identified in sequenced genomes) in target reactions of industrial interest. However, while many thousands of entries in the Protein Data Bank include molecular coordinates of P450 enzymes, only 19 entries correspond to UPO enzymes, and UPO structures from only two species (Agrocybe aegerita and Hypoxylon sp.) have been published to date. In the present study, two UPOs from the basidiomycete Marasmius rotula (rMroUPO) and the ascomycete Collariella virescens (rCviUPO) were crystallized after sequence optimization and Escherichia coli expression as active soluble enzymes. Crystals of rMroUPO and rCviUPO were obtained at sufficiently high resolution (1.45 and 1.95 Å, respectively) and the corresponding structures were solved by molecular replacement. The crystal structures of the two enzymes (and two mutated variants) showed dimeric proteins. Complementary biophysical and molecular biology studies unveiled the diverse structural bases of the dimeric nature of the two enzymes. Intermolecular disulfide bridge and parallel association between two α-helices, among other interactions, were identified at the dimer interfaces. Interestingly, one of the rCviUPO variants incorporated the ability to produce fatty acid diepoxides—reactive compounds with valuable cross-linking capabilities—due to removal of the enzyme C-terminal tail located near the entrance of the heme access channel. In conclusion, different dimeric arrangements could be described in (short) UPO crystal structures.

show abstract

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

Cited by 118 publications

References 103 publications

Selective Biocatalytic Defunctionalization of Raw Materials

Selective Biocatalytic Defunctionalization of Raw Materials

Catechin Mediates Ferroptosis to Exert an Anti-Inflammatory Effect on RAW 264.7 Cells

Structural Characterization of Two Short Unspecific Peroxygenases: Two Different Dimeric Arrangements

Contact Info

Product

Resources

About