4nsp

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Crystal structure of human ENDOV

Structural highlights

4nsp is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ENDOV_HUMAN Endoribonuclease that specifically cleaves inosine-containing RNAs: cleaves RNA at the second phosphodiester bond 3' to inosine. Has strong preference for single-stranded RNAs (ssRNAs) toward double-stranded RNAs (dsRNAs). Cleaves mRNAs and tRNAs containing inosine. Also able to cleave structure-specific dsRNA substrates containing the specific sites 5'-IIUI-3' and 5'-UIUU-3'. Inosine is present in a number of RNAs following editing; the function of inosine-specific endoribonuclease is still unclear: it could either play a regulatory role in edited RNAs, or be involved in antiviral response by removing the hyperedited long viral dsRNA genome that has undergone A-to-I editing. Binds branched DNA structures.[1] [2] [3]

Publication Abstract from PubMed

The 6-aminopurine ring of adenosine (A) can be deaminated to form the 6-oxopurine of inosine (I). Endonuclease Vs (EndoVs) are inosine-specific nucleases that cleave at the second phosphodiester bond 3' to inosine. EndoV proteins are highly conserved in all domains of life, but the bacterial and human enzymes seem to display distinct substrate preferences. While the bacterial enzymes exhibit high cleavage efficiency on various nucleic acid substrates, human EndoV (hEndoV) is most active towards ssRNA but is much less active towards other substrates. However, the structural basis of substrate recognition by hEndoV is not well understood. In this study, the 2.3 A resolution crystal structure of hEndoV was determined and its unusual RNA-cleaving properties were investigated. The enzyme preserves the general `RNase H-like' structure, especially in the wedge motif, the metal-binding site and the hypoxanthine-binding pocket. hEndoV also features several extra insertions and a characteristic four-cysteine motif, in which Cys227 and Cys228, two cysteines that are highly conserved in higher eukaryotes, play important roles in catalysis. The structure presented here helps in understanding the substrate preference of hEndoV catalysis.

Structure of human endonuclease V as an inosine-specific ribonuclease.,Zhang Z, Hao Z, Wang Z, Li Q, Xie W Acta Crystallogr D Biol Crystallogr. 2014 Sep 1;70(Pt 9):2286-94. doi:, 10.1107/S139900471401356X. Epub 2014 Aug 29. PMID:25195743[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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Citations
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Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Wu et al. (2019)
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3 other articles
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See Also

References

  1. ↑ Fladeby C, Vik ES, Laerdahl JK, Gran Neurauter C, Heggelund JE, Thorgaard E, Strom-Andersen P, Bjoras M, Dalhus B, Alseth I. The human homolog of Escherichia coli endonuclease V is a nucleolar protein with affinity for branched DNA structures. PLoS One. 2012;7(11):e47466. doi: 10.1371/journal.pone.0047466. Epub 2012 Nov 5. PMID:23139746 doi:http://dx.doi.org/10.1371/journal.pone.0047466
  2. ↑ Vik ES, Nawaz MS, Strom Andersen P, Fladeby C, Bjoras M, Dalhus B, Alseth I. Endonuclease V cleaves at inosines in RNA. Nat Commun. 2013;4:2271. doi: 10.1038/ncomms3271. PMID:23912683 doi:http://dx.doi.org/10.1038/ncomms3271
  3. ↑ Morita Y, Shibutani T, Nakanishi N, Nishikura K, Iwai S, Kuraoka I. Human endonuclease V is a ribonuclease specific for inosine-containing RNA. Nat Commun. 2013;4:2273. doi: 10.1038/ncomms3273. PMID:23912718 doi:http://dx.doi.org/10.1038/ncomms3273
  4. ↑ Zhang Z, Hao Z, Wang Z, Li Q, Xie W. Structure of human endonuclease V as an inosine-specific ribonuclease. Acta Crystallogr D Biol Crystallogr. 2014 Sep 1;70(Pt 9):2286-94. doi:, 10.1107/S139900471401356X. Epub 2014 Aug 29. PMID:25195743 doi:http://dx.doi.org/10.1107/S139900471401356X

Contents


PDB ID 4nsp

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