IPA9_SHIFL
ID IPA9_SHIFL Reviewed; 545 AA.
AC Q8VSC3; O85159; Q2TH74; Q6XVV1; Q9AFM5; Q9AJV1;
DT 13-JUL-2010, integrated into UniProtKB/Swiss-Prot.
DT 04-JAN-2005, sequence version 2.
DT 25-MAY-2022, entry version 114.
DE RecName: Full=E3 ubiquitin-protein ligase ipaH9.8;
DE EC=2.3.2.27;
DE AltName: Full=Invasion plasmid antigen ipaH9.8;
DE AltName: Full=RING-type E3 ubiquitin transferase ipaH9.8 {ECO:0000305};
GN Name=ipaH9.8; OrderedLocusNames=CP0226; ORFNames=pWR501_0234, SFLP090;
OS Shigella flexneri.
OG Plasmid pCP301, Plasmid pWR100, Plasmid pINV_F6_M1382, and Plasmid pSF5.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Shigella.
OX NCBI_TaxID=623;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-12 AND 480-494,
RP AND INDUCTION.
RC STRAIN=M90T / Serotype 5a; PLASMID=pWR100;
RX PubMed=9582283; DOI=10.1093/emboj/17.10.2894;
RA Demers B., Sansonetti P.J., Parsot C.;
RT "Induction of type III secretion in Shigella flexneri is associated with
RT differential control of transcription of genes encoding secreted
RT proteins.";
RL EMBO J. 17:2894-2903(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-9, AND SUBCELLULAR
RP LOCATION.
RC STRAIN=M90T / Serotype 5a; PLASMID=pWR100;
RX PubMed=11115111; DOI=10.1046/j.1365-2958.2000.02179.x;
RA Buchrieser C., Glaser P., Rusniok C., Nedjari H., d'Hauteville H.,
RA Kunst F., Sansonetti P.J., Parsot C.;
RT "The virulence plasmid pWR100 and the repertoire of proteins secreted by
RT the type III secretion apparatus of Shigella flexneri.";
RL Mol. Microbiol. 38:760-771(2000).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=M90T / Serotype 5a; PLASMID=pWR100;
RX PubMed=11292750; DOI=10.1128/iai.69.5.3271-3285.2001;
RA Venkatesan M.M., Goldberg M.B., Rose D.J., Grotbeck E.J., Burland V.,
RA Blattner F.R.;
RT "Complete DNA sequence and analysis of the large virulence plasmid of
RT Shigella flexneri.";
RL Infect. Immun. 69:3271-3285(2001).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=M1382 / Serotype 6; PLASMID=pINV_F6_M1382;
RX PubMed=14573649; DOI=10.1128/iai.71.11.6298-6306.2003;
RA Lan R., Stevenson G., Reeves P.R.;
RT "Comparison of two major forms of the Shigella virulence plasmid pINV:
RT positive selection is a major force driving the divergence.";
RL Infect. Immun. 71:6298-6306(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=Serotype 5; PLASMID=pSF5;
RX PubMed=16704117; DOI=10.1007/s11427-006-0141-3;
RA Xiong Z., Tang X., Yang F., Zhang X., Yang J., Chen L., Nie H., Yan Y.,
RA Jiang Y., Wang J., Xue Y., Xu X., Zhu Y., Dong J., An L., Wang X., Jin Q.;
RT "Comparison of the virulence plasmid genomes of two strains of Shigella
RT which lost the ability to bind Congo red.";
RL Sci. China, Ser. C, Life Sci. 49:141-148(2006).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=301 / Serotype 2a; PLASMID=pCP301;
RX PubMed=12384590; DOI=10.1093/nar/gkf566;
RA Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J.,
RA Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L.,
RA Xue Y., Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H.,
RA Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J.;
RT "Genome sequence of Shigella flexneri 2a: insights into pathogenicity
RT through comparison with genomes of Escherichia coli K12 and O157.";
RL Nucleic Acids Res. 30:4432-4441(2002).
RN [7]
RP SUBCELLULAR LOCATION, AND SECRETION VIA TYPE III SECRETION SYSTEM.
RC STRAIN=YSH6000 / Serotype 2a;
RX PubMed=11418613; DOI=10.1074/jbc.m101882200;
RA Toyotome T., Suzuki T., Kuwae A., Nonaka T., Fukuda H., Imajoh-Ohmi S.,
RA Toyofuku T., Hori M., Sasakawa C.;
RT "Shigella protein IpaH(9.8) is secreted from bacteria within mammalian
RT cells and transported to the nucleus.";
RL J. Biol. Chem. 276:32071-32079(2001).
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, AND INTERACTION WITH MURINE U2AF1.
RC STRAIN=YSH6000 / Serotype 2a;
RX PubMed=15950937; DOI=10.1016/j.bbrc.2005.05.145;
RA Okuda J., Toyotome T., Kataoka N., Ohno M., Abe H., Shimura Y.,
RA Seyedarabi A., Pickersgill R., Sasakawa C.;
RT "Shigella effector IpaH9.8 binds to a splicing factor U2AF(35) to modulate
RT host immune responses.";
RL Biochem. Biophys. Res. Commun. 333:531-539(2005).
RN [9]
RP FUNCTION AS A LIGASE, AND MUTAGENESIS OF CYS-337.
RX PubMed=18005683; DOI=10.1016/j.chom.2007.02.002;
RA Rohde J.R., Breitkreutz A., Chenal A., Sansonetti P.J., Parsot C.;
RT "Type III secretion effectors of the IpaH family are E3 ubiquitin
RT ligases.";
RL Cell Host Microbe 1:77-83(2007).
RN [10]
RP FUNCTION, INTERACTION WITH HOST IKBKG AND TNIP1, AND MUTAGENESIS OF
RP CYS-337.
RC STRAIN=YSH6000 / Serotype 2a;
RX PubMed=20010814; DOI=10.1038/ncb2006;
RA Ashida H., Kim M., Schmidt-Supprian M., Ma A., Ogawa M., Sasakawa C.;
RT "A bacterial E3 ubiquitin ligase IpaH9.8 targets NEMO/IKKgamma to dampen
RT the host NF-kappaB-mediated inflammatory response.";
RL Nat. Cell Biol. 12:66-73(2010).
RN [11]
RP MUTAGENESIS OF ARG-163; PHE-187; HIS-210 AND CYS-337, ACTIVE SITE, AND
RP FUNCTION.
RC STRAIN=M90T / Serotype 5a; PLASMID=pWR100;
RX PubMed=24248594; DOI=10.1128/mcb.01360-13;
RA Keszei A.F., Tang X., McCormick C., Zeqiraj E., Rohde J.R., Tyers M.,
RA Sicheri F.;
RT "Structure of an SspH1-PKN1 complex reveals the basis for host substrate
RT recognition and mechanism of activation for a bacterial E3 ubiquitin
RT ligase.";
RL Mol. Cell. Biol. 34:362-373(2014).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (3.20 ANGSTROMS) OF 254-545, FUNCTION, INTERACTION
RP WITH HUMAN U2AF1, AUTOUBIQUITINATION, AND ACTIVITY REGULATION.
RC STRAIN=YSH6000 / Serotype 2a;
RX PubMed=20831869; DOI=10.1016/j.febslet.2010.09.006;
RA Seyedarabi A., Sullivan J.A., Sasakawa C., Pickersgill R.W.;
RT "A disulfide driven domain swap switches off the activity of Shigella
RT IpaH9.8 E3 ligase.";
RL FEBS Lett. 584:4163-4168(2010).
CC -!- FUNCTION: Effector proteins function to alter host cell physiology and
CC promote bacterial survival in host tissues. This protein is an E3
CC ubiquitin ligase that interferes with host's ubiquitination pathway and
CC modulates the acute inflammatory responses, thus facilitating bacterial
CC colonization within the host cell. Interacts with IKBKG (NEMO) and
CC TNIP1 (ABIN-1), a ubiquitin-binding adapter protein, which results in
CC TNIP1-dependent 'Lys-27'-linked polyubiquitination of IKBKG.
CC Consequently, polyubiquitinated IKBKG undergoes proteasome-dependent
CC degradation, which perturbs NF-kappa-B activation during bacterial
CC infection. Uses UBE2D2 (UBCH5B) as an E2 ubiquitin-conjugating enzyme.
CC Mediates polyubiquitination of host U2AF1, leading to its proteasomal
CC degradation. {ECO:0000269|PubMed:15950937, ECO:0000269|PubMed:18005683,
CC ECO:0000269|PubMed:20010814, ECO:0000269|PubMed:20831869,
CC ECO:0000269|PubMed:24248594}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine +
CC [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-
CC cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.;
CC EC=2.3.2.27;
CC -!- ACTIVITY REGULATION: Exists in an autoinhibited state in the absence of
CC substrate protein, probably due to interactions of the leucine-rich
CC repeat domain with the catalytic domain. Is activated upon binding to a
CC substrate protein. {ECO:0000269|PubMed:20831869}.
CC -!- SUBUNIT: Interacts with human IKBKG (NEMO) and TNIP1 (ABIN-1).
CC Interacts also with human and murine U2AF1 (U2AF35).
CC {ECO:0000269|PubMed:15950937, ECO:0000269|PubMed:20010814,
CC ECO:0000269|PubMed:20831869}.
CC -!- INTERACTION:
CC Q8VSC3; Q8VSC3: ipaH9.8; NbExp=3; IntAct=EBI-6125799, EBI-6125799;
CC Q8VSC3; Q9Y6K9: IKBKG; Xeno; NbExp=8; IntAct=EBI-6125799, EBI-81279;
CC Q8VSC3; Q15025: TNIP1; Xeno; NbExp=4; IntAct=EBI-6125799, EBI-357849;
CC -!- SUBCELLULAR LOCATION: Secreted {ECO:0000269|PubMed:11115111}. Host
CC cytoplasm {ECO:0000269|PubMed:11418613}. Host nucleus
CC {ECO:0000269|PubMed:11418613}. Note=Secreted via Mxi-Spa type III
CC secretion system (TTSS), and delivered into the host cytoplasm
CC (PubMed:11115111, PubMed:11418613). Transported into the host nucleus
CC (PubMed:11418613). This transport is independent of cytosolic factors,
CC but dependent on temperature and partly on ATP/GTP (PubMed:11418613).
CC {ECO:0000269|PubMed:11115111, ECO:0000269|PubMed:11418613}.
CC -!- INDUCTION: Induced upon entry into host epithelial cells.
CC {ECO:0000269|PubMed:9582283}.
CC -!- DOMAIN: The LRR (leucine-rich repeat) domain forms a slightly curved
CC solenoid and may mediate interaction with target proteins.
CC {ECO:0000250|UniProtKB:P0CE12}.
CC -!- PTM: Autoubiquitinated (in vitro). Ubiquitinated in the presence of
CC host E1 ubiquitin-activating enzyme, E2 ubiquitin-conjugating enzyme
CC and ubiquitin. {ECO:0000269|PubMed:20831869}.
CC -!- DISRUPTION PHENOTYPE: In murine lung infection model, mutants cause
CC severe inflammatory responses, with increased pro-inflammatory cytokine
CC production levels. Colonization is greatly reduced.
CC {ECO:0000269|PubMed:15950937}.
CC -!- SIMILARITY: Belongs to the LRR-containing bacterial E3 ligase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAK18544.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAW64849.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AF047365; AAC23714.1; -; Genomic_DNA.
DR EMBL; AL391753; CAC05853.1; -; Genomic_DNA.
DR EMBL; AF348706; AAK18544.1; ALT_INIT; Genomic_DNA.
DR EMBL; AY206445; AAP79029.1; -; Genomic_DNA.
DR EMBL; AY879342; AAW64849.1; ALT_INIT; Genomic_DNA.
DR EMBL; AF386526; AAL72345.2; -; Genomic_DNA.
DR RefSeq; NP_858359.2; NC_004851.1.
DR RefSeq; WP_010921715.1; NC_019197.1.
DR RefSeq; YP_006960318.1; NC_019197.1.
DR PDB; 3L3P; X-ray; 3.20 A; A=254-545.
DR PDB; 5B0N; X-ray; 1.80 A; A/B=22-244.
DR PDB; 5B0T; X-ray; 2.00 A; A=22-244.
DR PDB; 6K2D; X-ray; 3.60 A; B=22-252.
DR PDBsum; 3L3P; -.
DR PDBsum; 5B0N; -.
DR PDBsum; 5B0T; -.
DR PDBsum; 6K2D; -.
DR AlphaFoldDB; Q8VSC3; -.
DR SMR; Q8VSC3; -.
DR DIP; DIP-46341N; -.
DR IntAct; Q8VSC3; 3.
DR MINT; Q8VSC3; -.
DR STRING; 198214.SF1880; -.
DR EnsemblBacteria; AAL72345; AAL72345; SF_p0226.
DR GeneID; 1238048; -.
DR KEGG; sfl:CP0226; -.
DR PATRIC; fig|198214.7.peg.5483; -.
DR HOGENOM; CLU_018533_2_0_6; -.
DR PRO; PR:Q8VSC3; -.
DR Proteomes; UP000001006; Plasmid pCP301.
DR GO; GO:0005576; C:extracellular region; IDA:UniProtKB.
DR GO; GO:0044164; C:host cell cytosol; IDA:UniProtKB.
DR GO; GO:0042025; C:host cell nucleus; IDA:UniProtKB.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0061630; F:ubiquitin protein ligase activity; IDA:GO_Central.
DR GO; GO:0004842; F:ubiquitin-protein transferase activity; IDA:UniProtKB.
DR GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IDA:GO_Central.
DR GO; GO:0051865; P:protein autoubiquitination; IDA:CACAO.
DR GO; GO:0044314; P:protein K27-linked ubiquitination; IDA:UniProtKB.
DR GO; GO:0085034; P:suppression by symbiont of host I-kappaB kinase/NF-kappaB cascade; IDA:GO_Central.
DR GO; GO:0052036; P:suppression by symbiont of host inflammatory response; IDA:GO_Central.
DR Gene3D; 3.80.10.10; -; 1.
DR InterPro; IPR032675; LRR_dom_sf.
DR InterPro; IPR032674; LRR_E3_ligase_N.
DR InterPro; IPR029487; NEL_dom.
DR Pfam; PF14496; NEL; 1.
DR Pfam; PF12468; TTSSLRR; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Host cytoplasm; Host nucleus;
KW Leucine-rich repeat; Plasmid; Reference proteome; Repeat; Secreted;
KW Transferase; Ubl conjugation; Ubl conjugation pathway; Virulence.
FT CHAIN 1..545
FT /note="E3 ubiquitin-protein ligase ipaH9.8"
FT /id="PRO_0000395755"
FT REPEAT 57..77
FT /note="LRR 1"
FT REPEAT 78..99
FT /note="LRR 2"
FT REPEAT 100..117
FT /note="LRR 3"
FT REPEAT 118..139
FT /note="LRR 4"
FT REPEAT 140..157
FT /note="LRR 5"
FT REPEAT 158..179
FT /note="LRR 6"
FT REPEAT 182..203
FT /note="LRR 7"
FT REPEAT 205..228
FT /note="LRR 8"
FT REGION 1..242
FT /note="Interaction with target proteins"
FT /evidence="ECO:0000250|UniProtKB:P0CE12"
FT REGION 243..250
FT /note="Linker"
FT /evidence="ECO:0000250|UniProtKB:P0CE12"
FT REGION 251..545
FT /note="E3 ubiquitin-protein ligase catalytic domain"
FT /evidence="ECO:0000250|UniProtKB:P0CE12"
FT ACT_SITE 337
FT /note="Glycyl thioester intermediate"
FT /evidence="ECO:0000269|PubMed:24248594"
FT VARIANT 222
FT /note="P -> Q (in plasmid pWR100, plasmid pSF5 and plasmid
FT pINV_F6_M1382)"
FT VARIANT 474
FT /note="Q -> L (in plasmid pINV_F6_M1382)"
FT VARIANT 536
FT /note="P -> F (in plasmid pWR100)"
FT VARIANT 536
FT /note="P -> S (in plasmid pSF5)"
FT MUTAGEN 163
FT /note="R->A: Abolishes proteasomal degradation of host
FT proteins; when associated with A-187 and A-210."
FT /evidence="ECO:0000269|PubMed:24248594"
FT MUTAGEN 187
FT /note="F->A: Abolishes proteasomal degradation of host
FT proteins; when associated with A-163 and A-210."
FT /evidence="ECO:0000269|PubMed:24248594"
FT MUTAGEN 210
FT /note="H->A: Abolishes proteasomal degradation of host
FT proteins; when associated with A-163 and A-187."
FT /evidence="ECO:0000269|PubMed:24248594"
FT MUTAGEN 337
FT /note="C->A: Abolishes proteasomal degradation of host
FT proteins."
FT /evidence="ECO:0000269|PubMed:18005683,
FT ECO:0000269|PubMed:20010814, ECO:0000269|PubMed:24248594"
FT MUTAGEN 337
FT /note="C->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:18005683,
FT ECO:0000269|PubMed:20010814, ECO:0000269|PubMed:24248594"
FT CONFLICT 7
FT /note="Missing (in Ref. 2; AA sequence)"
FT /evidence="ECO:0000305"
FT HELIX 23..35
FT /evidence="ECO:0007829|PDB:5B0N"
FT HELIX 43..55
FT /evidence="ECO:0007829|PDB:5B0N"
FT STRAND 59..62
FT /evidence="ECO:0007829|PDB:5B0N"
FT STRAND 80..83
FT /evidence="ECO:0007829|PDB:5B0N"
FT STRAND 101..103
FT /evidence="ECO:0007829|PDB:5B0N"
FT STRAND 121..123
FT /evidence="ECO:0007829|PDB:5B0N"
FT STRAND 141..143
FT /evidence="ECO:0007829|PDB:5B0N"
FT STRAND 161..163
FT /evidence="ECO:0007829|PDB:5B0N"
FT STRAND 185..187
FT /evidence="ECO:0007829|PDB:5B0N"
FT HELIX 198..201
FT /evidence="ECO:0007829|PDB:5B0N"
FT STRAND 208..210
FT /evidence="ECO:0007829|PDB:5B0N"
FT HELIX 220..229
FT /evidence="ECO:0007829|PDB:5B0N"
FT STRAND 237..239
FT /evidence="ECO:0007829|PDB:5B0N"
FT HELIX 254..259
FT /evidence="ECO:0007829|PDB:3L3P"
FT HELIX 264..273
FT /evidence="ECO:0007829|PDB:3L3P"
FT HELIX 274..276
FT /evidence="ECO:0007829|PDB:3L3P"
FT HELIX 283..293
FT /evidence="ECO:0007829|PDB:3L3P"
FT HELIX 305..318
FT /evidence="ECO:0007829|PDB:3L3P"
FT HELIX 320..359
FT /evidence="ECO:0007829|PDB:3L3P"
FT HELIX 366..386
FT /evidence="ECO:0007829|PDB:3L3P"
FT TURN 387..389
FT /evidence="ECO:0007829|PDB:3L3P"
FT HELIX 400..408
FT /evidence="ECO:0007829|PDB:3L3P"
FT TURN 409..414
FT /evidence="ECO:0007829|PDB:3L3P"
FT HELIX 434..448
FT /evidence="ECO:0007829|PDB:3L3P"
FT HELIX 451..455
FT /evidence="ECO:0007829|PDB:3L3P"
FT HELIX 458..466
FT /evidence="ECO:0007829|PDB:3L3P"
FT HELIX 469..484
FT /evidence="ECO:0007829|PDB:3L3P"
FT HELIX 486..498
FT /evidence="ECO:0007829|PDB:3L3P"
FT HELIX 504..530
FT /evidence="ECO:0007829|PDB:3L3P"
SQ SEQUENCE 545 AA; 61979 MW; 5E70042D797B5099 CRC64;
MLPINNNFSL PQNSFYNTIS GTYADYFSAW DKWEKQALPG EERDEAVSRL KECLINNSDE
LRLDRLNLSS LPDNLPAQIT LLNVSYNQLT NLPELPVTLK KLYSASNKLS ELPVLPPALE
SLQVQHNELE NLPALPDSLL TMNISYNEIV SLPSLPQALK NLRATRNFLT ELPAFSEGNN
PVVREYFFDR NQISHIPESI LNLRNECSIH ISDNPLSSHA LPALQRLTSS PDYHGPRIYF
SMSDGQQNTL HRPLADAVTA WFPENKQSDV SQIWHAFEHE EHANTFSAFL DRLSDTVSAR
NTSGFREQVA AWLEKLSASA ELRQQSFAVA ADATESCEDR VALTWNNLRK TLLVHQASEG
LFDNDTGALL SLGREMFRLE ILEDIARDKV RTLHFVDEIE VYLAFQTMLA EKLQLSTAVK
EMRFYGVSGV TANDLRTAEA MVRSREENEF TDWFSLWGPW HAVLKRTEAD RWAQAEEQKY
EMLENEYPQR VADRLKASGL SGDADAEREA GAQVMRETEQ QIYRQLTDEV LALRLPENGS
QLHHS
