PDZscape: a comprehensive PDZ-protein database

Doshi, Jitesh; Kuppili, Raja Reddy; Gurdasani, Siddharth; Venkatakrishnan, Navneet; Saxena, Amit; Bose, Kakoli

doi:10.1186/s12859-018-2156-8

Cited by 3 publications

(3 citation statements)

References 14 publications

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“…E6 of HPV 16 has the PDZ-binding motif (PBM), a specific sequence located at the carboxy-terminal end that interacts with PDZ-domain-containing proteins [ 58 ]. VHL was observed to have sequence homology to PDZ compared to the 58,648 proteins in the PDZ scape database library [ 46 ]. The predicted PDZ in VHL has a higher identity score (37.7) than the PDZ score of E6-AP (30.6).…”

Section: Discussionmentioning

confidence: 99%

“…PDZ domain search was performed in the PDZscape database ( accessed on 5 October 2023). PDZscape encompasses the complete information available on 58,648 PDZ-containing proteins with their known and putative binding partners in one platform, with a unique integration of prominent databases, including NCBI, UniProtKB, Swiss-Prot, Pubmed, PDB, STRING, IntAct, KEGG, Pfam, and the Protein Mutant Database, providing detailed information on the PDZ interactome in addition to the custom BLAST option [ 46 ].…”

Section: Methodsmentioning

confidence: 99%

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Bioinformatics Analysis Reveals E6 and E7 of HPV 16 Regulate Metabolic Reprogramming in Cervical Cancer, Head and Neck Cancer, and Colorectal Cancer through the PHD2-VHL-CUL2-ELOC-HIF-1α Axis

Arizmendi-Izazaga,

Navarro-Tito,

Jiménez-Wences

et al. 2024

CIMB

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Human papillomavirus 16 (HPV 16) infection is associated with several types of cancer, such as head and neck, cervical, anal, and penile cancer. Its oncogenic potential is due to the ability of the E6 and E7 oncoproteins to promote alterations associated with cell transformation. HPV 16 E6 and E7 oncoproteins increase metabolic reprogramming, one of the hallmarks of cancer, by increasing the stability of hypoxia-induced factor 1 α (HIF-1α) and consequently increasing the expression levels of their target genes. In this report, by bioinformatic analysis, we show the possible effect of HPV 16 oncoproteins E6 and E7 on metabolic reprogramming in cancer through the E6-E7-PHD2-VHL-CUL2-ELOC-HIF-1α axis. We proposed that E6 and E7 interact with VHL, CUL2, and ELOC in forming the E3 ubiquitin ligase complex that ubiquitinates HIF-1α for degradation via the proteasome. Based on the information found in the databases, it is proposed that E6 interacts with VHL by blocking its interaction with HIF-1α. On the other hand, E7 interacts with CUL2 and ELOC, preventing their binding to VHL and RBX1, respectively. Consequently, HIF-1α is stabilized and binds with HIF-1β to form the active HIF1 complex that binds to hypoxia response elements (HREs), allowing the expression of genes related to energy metabolism. In addition, we suggest an effect of E6 and E7 at the level of PHD2, VHL, CUL2, and ELOC gene expression. Here, we propose some miRNAs targeting PHD2, VHL, CUL2, and ELOC mRNAs. The effect of E6 and E7 may be the non-hydroxylation and non-ubiquitination of HIF-1α, which may regulate metabolic processes involved in metabolic reprogramming in cancer upon stabilization, non-degradation, and translocation to the nucleus.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Bioinformatics Analysis Reveals E6 and E7 of HPV 16 Regulate Metabolic Reprogramming in Cervical Cancer, Head and Neck Cancer, and Colorectal Cancer through the PHD2-VHL-CUL2-ELOC-HIF-1α Axis

Arizmendi-Izazaga,

Navarro-Tito,

Jiménez-Wences

et al. 2024

CIMB

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“…Despite low overall sequence identity, HtrA proteins can be identified relatively using the PDZscape database [27] . Making use of HtrA protein sequences from 25 representative pathogenic bacteria, we undertook a phylogenetic analysis and Ancestor Sequence Reconstruction (ASR) [28] .…”

Section: Distribution and Evolution Of Htra Family Proteins In Pathogenic Bacteriamentioning

confidence: 99%

Function, molecular mechanisms, and therapeutic potential of bacterial HtrA proteins: An evolving view

Song

Kang

et al. 2022

Computational and Structural Biotechnology Journal

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Members of the high temperature requirement A (HtrA) protein family are widely distributed amongst prokaryotic and eukaryotic species. HtrA proteins have ATP-independent dual chaperone-protease activity and mediate protein quality control. Emerging evidence indicates that HtrA family members are vital for establishing infections and bacterial survival under stress conditions. Bacterial HtrA proteins are increasingly thought of as important new targets for antibacterial drug development. Recent literature suggests that HtrA protein AlgW from Pseudomonas aeruginosa has distinct structural, functional, and regulatory characteristics. The novel dual-signal activation mechanism seen in AlgW is required to modulate stress and drug responses in bacteria, prompting us to review our understanding of the many HtrA proteins found in microorganisms. Here, we describe the distribution of HtrA gene orthologues in pathogenic bacteria, discuss their structure–function relationships, outline the molecular mechanisms exhibited by different bacterial HtrA proteins in bacteria under selective pressure, and review the significance of recently developed small molecule inhibitors targeting HtrA in pathogenic bacteria.

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PICK1 modulates glycolysis and angiogenesis of hypoxic endothelial cells by regulating iron homeostasis

Cao

Wang

et al. 2023

Mol Cell Biochem

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PDZscape: a comprehensive PDZ-protein database

Cited by 3 publications

References 14 publications

Bioinformatics Analysis Reveals E6 and E7 of HPV 16 Regulate Metabolic Reprogramming in Cervical Cancer, Head and Neck Cancer, and Colorectal Cancer through the PHD2-VHL-CUL2-ELOC-HIF-1α Axis

Bioinformatics Analysis Reveals E6 and E7 of HPV 16 Regulate Metabolic Reprogramming in Cervical Cancer, Head and Neck Cancer, and Colorectal Cancer through the PHD2-VHL-CUL2-ELOC-HIF-1α Axis

Function, molecular mechanisms, and therapeutic potential of bacterial HtrA proteins: An evolving view

PICK1 modulates glycolysis and angiogenesis of hypoxic endothelial cells by regulating iron homeostasis

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