VAPD_HELPY
ID VAPD_HELPY Reviewed; 94 AA.
AC O05728;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 25-MAY-2022, entry version 99.
DE RecName: Full=Endoribonuclease VapD;
DE EC=3.1.-.-;
DE AltName: Full=Virulence-associated protein D;
GN Name=vapD; OrderedLocusNames=HP_0315;
OS Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=85962;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 49503 / 60190;
RX PubMed=9139899; DOI=10.1128/jb.179.9.2852-2856.1997;
RA Cao P., Cover T.L.;
RT "High-level genetic diversity in the vapD chromosomal region of
RT Helicobacter pylori.";
RL J. Bacteriol. 179:2852-2856(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700392 / 26695;
RX PubMed=9252185; DOI=10.1038/41483;
RA Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G.,
RA Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A.,
RA Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N.,
RA Loftus B.J., Richardson D.L., Dodson R.J., Khalak H.G., Glodek A.,
RA McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E.,
RA Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D.,
RA Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S.,
RA Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.;
RT "The complete genome sequence of the gastric pathogen Helicobacter
RT pylori.";
RL Nature 388:539-547(1997).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), FUNCTION AS AN ENDORIBONUCLEASE,
RP SUBUNIT, AND MUTAGENESIS OF ASP-7; LEU-13; PHE-37; SER-43; VAL-74 AND
RP ASP-76.
RC STRAIN=ATCC 700392 / 26695;
RX PubMed=22241770; DOI=10.1093/nar/gkr1305;
RA Kwon A.R., Kim J.H., Park S.J., Lee K.Y., Min Y.H., Im H., Lee I.,
RA Lee K.Y., Lee B.J.;
RT "Structural and biochemical characterization of HP0315 from Helicobacter
RT pylori as a VapD protein with an endoribonuclease activity.";
RL Nucleic Acids Res. 40:4216-4228(2012).
CC -!- FUNCTION: Cleaves ssRNA, mostly between U:A; cleavage is not dependent
CC on mono- or divalent cations. Can cleave RNAs as short as 6
CC nucleotides. {ECO:0000269|PubMed:22241770}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:22241770}.
CC -!- MISCELLANEOUS: There is no VapD ortholog in strain J99.
CC -!- SIMILARITY: Belongs to the VapD ribonuclease family. {ECO:0000305}.
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DR EMBL; U94318; AAC45241.1; -; Genomic_DNA.
DR EMBL; AE000511; AAD07379.1; -; Genomic_DNA.
DR PIR; C64559; C64559.
DR PIR; T09450; T09450.
DR RefSeq; NP_207113.1; NC_000915.1.
DR RefSeq; WP_000271050.1; NC_018939.1.
DR PDB; 3UI3; X-ray; 2.80 A; A/B=1-94.
DR PDBsum; 3UI3; -.
DR AlphaFoldDB; O05728; -.
DR SMR; O05728; -.
DR STRING; 85962.C694_01590; -.
DR PaxDb; O05728; -.
DR EnsemblBacteria; AAD07379; AAD07379; HP_0315.
DR KEGG; hpy:HP_0315; -.
DR PATRIC; fig|85962.47.peg.335; -.
DR eggNOG; COG3309; Bacteria.
DR OMA; NMNEDMA; -.
DR PhylomeDB; O05728; -.
DR Proteomes; UP000000429; Chromosome.
DR GO; GO:0004518; F:nuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR InterPro; IPR016368; VapD.
DR InterPro; IPR019199; Virulence_VapD/CRISPR_Cas2.
DR Pfam; PF09827; CRISPR_Cas2; 1.
DR PIRSF; PIRSF002882; VapD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Nuclease; Reference proteome; RNA-binding;
KW Virulence.
FT CHAIN 1..94
FT /note="Endoribonuclease VapD"
FT /id="PRO_0000217272"
FT MUTAGEN 7
FT /note="D->A: Significantly reduced ribonuclease activity."
FT /evidence="ECO:0000269|PubMed:22241770"
FT MUTAGEN 13
FT /note="L->A: Nearly complete loss of ribonuclease
FT activity."
FT /evidence="ECO:0000269|PubMed:22241770"
FT MUTAGEN 37
FT /note="F->A: Protein unstable."
FT /evidence="ECO:0000269|PubMed:22241770"
FT MUTAGEN 43
FT /note="S->A: Nearly complete loss of ribonuclease
FT activity."
FT /evidence="ECO:0000269|PubMed:22241770"
FT MUTAGEN 74
FT /note="V->A: Protein unstable."
FT /evidence="ECO:0000269|PubMed:22241770"
FT MUTAGEN 76
FT /note="D->A: Significantly reduced ribonuclease activity."
FT /evidence="ECO:0000269|PubMed:22241770"
FT CONFLICT 18
FT /note="G -> K (in Ref. 1; AAC45241)"
FT /evidence="ECO:0000305"
FT CONFLICT 39
FT /note="W -> N (in Ref. 1; AAC45241)"
FT /evidence="ECO:0000305"
FT STRAND 1..8
FT /evidence="ECO:0007829|PDB:3UI3"
FT HELIX 10..16
FT /evidence="ECO:0007829|PDB:3UI3"
FT HELIX 22..34
FT /evidence="ECO:0007829|PDB:3UI3"
FT STRAND 37..40
FT /evidence="ECO:0007829|PDB:3UI3"
FT STRAND 43..47
FT /evidence="ECO:0007829|PDB:3UI3"
FT HELIX 53..65
FT /evidence="ECO:0007829|PDB:3UI3"
FT HELIX 68..73
FT /evidence="ECO:0007829|PDB:3UI3"
FT STRAND 74..87
FT /evidence="ECO:0007829|PDB:3UI3"
FT HELIX 89..93
FT /evidence="ECO:0007829|PDB:3UI3"
SQ SEQUENCE 94 AA; 11189 MW; 2475C5EBDF6F8FBF CRC64;
MYALAFDLKI EILKKEYGEP YNKAYDDLRQ ELELLGFEWT QGSVYVNYSK ENTLAQVYKA
INKLSQIEWF KKSVRDIRAF KVEDFSDFTE IVKS
