Dali server: structural unification of protein families

Holm, Liisa

doi:10.1093/nar/gkac387

Cited by 616 publications

(542 citation statements)

References 37 publications

(42 reference statements)

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“…The model building revealed a well resolved extra density between tracrRNA and Cas12k. A de novo built template model resulting from this extra density was subjected to a DALI (Holm, 2022) search and identified the prokaryotic ribosomal S15 protein as closely related. The E. coli ribosomal S15 protein was confirmed to have co-purified with TniQ by mass spectrometry (see also Table S2 ) and build in the extra density with great fit.…”

Section: Methodsmentioning

confidence: 99%

Structural basis for RNA-mediated assembly of type V CRISPR-associated transposons

Schmitz

Querques

Oberli

et al. 2022

Preprint

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CRISPR systems have been co-opted by Tn7-like elements to direct RNA-guided transposition. Type V-K CRISPR-associated transposons rely on the concerted activities of the pseudonuclease Cas12k, the AAA+ ATPase TnsC, the Zn-finger protein TniQ, and the transposase TnsB. Here we present a cryo-electron microscopic structure of a target DNA-bound Cas12k-transposon recruitment complex comprising RNA-guided Cas12k, TniQ, TnsC and, unexpectedly, the ribosomal protein S15. Complex assembly on target DNA results in complete R-loop formation mediated by critical interactions between TniQ and the trans-activating crRNA, and is coupled with TniQ-dependent nucleation of a TnsC filament. In vivo transposition assays corroborate our structural findings, and biochemical and functional analyses of S15 supports its role as a bona fide component of the type V crRNA-guided transposition machinery. Altogether, our work uncovers key aspects of the mechanisms underpinning RNA-mediated assembly of CRISPR-associated transposons that will guide their development as programmable site- specific gene insertion tools.

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Section: Methodsmentioning

confidence: 99%

Structural basis for RNA-mediated assembly of type V CRISPR-associated transposons

Schmitz

Querques

Oberli

et al. 2022

Preprint

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“…Iterative PsiBLAST 30 and HhPRED 31 searches detected two distant orphan clusters at 10-15% identity: i) YwaF proteins in bacteria and archaea (PF09529), and ii) TMEM164 proteins in animals (PF14808). The derivation of structurally accurate AlphaFold2 models 27 , either from proteome model databases 32 or built with ColabFold 33 , allowed for a broader structural comparison with DALI 34 unhindered by low to negligible sequence similarity that, in conjunction with reciprocal homology searches, linked the AIG1/ADTRP, YwaF, and TMEM164 families to additional bacterial/archaeal (YpjA) and protozoa (Hypothetical)) proteins ( Fig. 4a and Extended Data Fig.…”

Section: Resultsmentioning

confidence: 99%

TMEM164 is an acyltransferase that forms ferroptotic polyunsaturated ether phospholipids

Reed

Ware

et al. 2022

Preprint

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Ferroptosis is an iron-dependent form of cell death driven by the oxidation of polyunsaturated (PUFA) phospholipids. Large-scale genetic screens have pointed to a specialized role for PUFA ether phospholipids (ePLs) in promoting ferroptosis. Our understanding of the enzymes involved in PUFA ePL production, however, remains incomplete. Here we show using a combination of pathway mining of genetic dependency maps, AlphaFold-guided structure predictions, and targeted lipidomics that the uncharacterized transmembrane protein TMEM164 – genetic ablation of which has been shown to protect cells from ferroptosis – is a cysteine active-center enzyme that selectively transfers C20:4 acyl chains from phosphatidylcholine to lyso-ePLs to furnish PUFA-ePLs. TMEM164-null cells show substantial reductions in PUFA-ePLs, but not PUFA ester phospholipids, supporting that the selective suppression of PUFA-ePLs is sufficient to protect cells from ferroptosis and designating TMEM164 as a key enzyme specifically responsible for regulating this class of lipids.

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“…Recently, AlphaFold ( 11 ) structure predictions for almost all proteins of the human genome were made available at https://alphafold.ebi.ac.uk ( 12 ). We submitted the AlphaFold structure prediction for C12orf29, which was expected to be of high quality (average pLDDT = 91.4), to the Dali server ( 13 ), and compared it exhaustively to a representative subset of the Protein Data Bank. The results of structural superposition by Dali are highly significant and display RNA ligases as most similar structures (top hit, Z-score = 7.4 for Ngr Rnl), confirming our initial sequence-based suggestion for the functional assignment of C12orf29.…”

Section: Figmentioning

confidence: 99%

A human RNA ligase that operates via auto- and RNA-AMPylation

Yuan

Stumpf

Schlor

et al. 2022

Preprint

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Different forms of life are known to express RNA ligases that catalyze the condensation of a 3’-hydroxy group and a 5’-terminal phosphate of RNA. No such RNA ligases have yet been identified in vertebrates. Here, we report that the hitherto uncharacterized human protein chromosome 12 open reading frame 29 (C12orf29) is a 5’-3’ RNA ligase. C12orf29 catalyzes RNA ligation via auto-AMPylation of a critical lysine residue by using ATP as a cosubstrate and subsequent AMP transfer to the 5’-phosphate of an RNA substrate followed by phosphodiester bond formation. Studies at the cellular level reveal the involvement of C12orf29 in maintaining RNA integrity upon cellular stress induced by reactive oxygen species. These findings highlight the importance of RNA ligation for cellular fitness.One Sentence SummaryC12orf29, a protein of hitherto unknown function, is the first example of a human 5’-3’ RNA ligase that is involved in RNA maintenance and cellular resilience.

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Dali server: structural unification of protein families

Cited by 616 publications

References 37 publications

Structural basis for RNA-mediated assembly of type V CRISPR-associated transposons

Structural basis for RNA-mediated assembly of type V CRISPR-associated transposons

TMEM164 is an acyltransferase that forms ferroptotic polyunsaturated ether phospholipids

A human RNA ligase that operates via auto- and RNA-AMPylation

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