iUUCD 2.0 - integrated annotations for ubiquitin and ubiquitin-like conjugation database

Protein
Gene
Annotation
Details
Classification
Domain Profile
Function
Protein Sequence
Nucleotide Sequence
Keyword
GO
Orthology
TOP

Basic Information

Integrated Annotations

Tag

Content

iUUCD ID

IUUC-Sce-106247

UUCD1 version

UUC-SaC-00244

Ensembl Protein ID

YMR223W

UniProt Accession

P50102; D6W048; UBP8_YEAST

Genbank Protein ID

CAA90194.1; DAA10122.1

Protein Name

Ubiquitin carboxyl-terminal hydrolase 8; Deubiquitinating enzyme 8; Ubiquitin thioesterase 8; Ubiquitin-specific-processing protease 8

Genbank Nucleotide ID

Z49939; BK006946

Gene Name

UBP8; YMR223W; YM9959.05

Ensembl Information

Ensembl Gene ID	Ensembl Transcript ID	Ensembl Protein ID
YMR223W	YMR223W	YMR223W

Annotation

mRNA Expression
GEO	FFGED
Protein-protein Interaction
IID	iRefIndex	HINT	Mentha
Protein 3D Structure
PDB	MMDB
Protein Expression/Proteomics
GPMDB

Status

Reviewed

Details

Family	Domain	References (PMIDs)
DUB/USP	USP	14563679

Classification

Family	E-value	Score	Start	End
DUB/USP	4.40e-88	294.1	138	466

Active Site

Position(s)	Description	Evidence
146	Nucleophile
427	Proton acceptor	ECO:0000255\|PROSITE-ProRule:PRU10092, ECO:0000255\|PROSITE-ProRule:PRU10093}

Domain Profile

DUB/USP

   S: 2    GlkNlgNtCYmNSvLQcLsnipelrellle.kkkeklneenpkepkgellkslqklfeelw......kskkkavspre.........llkalkkeaeefsgy 87
           Gl N+g tC+m S+LQcL++ p + +   +  ++++++ +   +p+++++++l k+++el+      +    + s ++         ll++ +k+++++ gy
   Q: 138  GLINMGSTCFMSSILQCLIHNPYFIRHSMSqIHSNNCKVR---SPDKCFSCALDKIVHELYgalntkQ---ASSSSTStnrqtgfiyLLTCAWKINQNLAGY 233
           9***********************8777664777777765...78***************88764332...3222222445788888*************** PP
   S: 88   eqqDaqEflaflldqleeelkkeknkpkeeeeeedkselsdeaeekkkkknkslisdlFqgqlksqikclecdnvs.sreepfldlslpvpgkeetkkeslq 188
           +qqDa+Ef++f+++q++++        + ++ +       +e ++ ++k+ +++++++F+g+l+s+i+c+ c+n+s ++ +pfldlsl++++k+     +l 
   Q: 234  SQQDAHEFWQFIINQIHQSY-------VLDLPN------AKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSkTTIDPFLDLSLDIKDKK-----KLY 317
           ********************.......333322......234667899****************************999***************.....8** PP
   S: 189  dcLesftkeeelegenkyycekckkkqeaekklklkklPevLilhLkRfsfseeqksrekinkkvefpleLdlspfctspeekqke......kkkYeLiavv 284
           +cL+sf+k+e+l++ n y+c +c++ q+a k+l+++klP vL+l+LkRf+   + +s++k+++ +efp  L+++++c+++e+++++      + +YeLi++v
   Q: 318  ECLDSFHKKEQLKDFN-YHCGECNSTQDAIKQLGIHKLPSVLVLQLKRFEHLLN-GSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSengkvpDIIYELIGIV 417
           ************9765.********************************98886.8999********************8888777999999********** PP
   S: 285  vHsGslssGHYvayvknekgkWllfdDskVtevkeeevleetgstaYvlfYk 336
           +H+G++++GHY+a++k + g+W++f+Ds V+++++eevl+   ++aY+lfY+
   Q: 418  SHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLK---EQAYLLFYT 466
           ****************************************...********7 PP

Organism

Saccharomyces cerevisiae

Functional Description
(View)

Functions as histone deubiquitinating component of the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. Together with SGF11, is required for histone H2B deubiquitination.

Protein Sequence
(Fasta)

MSICPHIQQV FQNEKSKDGV LKTCNAARYI LNHSVPKEKF LNTMKCGTCH EINSGATFMC 60
LQCGFCGCWN HSHFLSHSKQ IGHIFGINSN NGLLFCFKCE DYIGNIDLIN DAILAKYWDD 120

It may take some time, please wait.

Nucleotide Sequence
(Fasta)

ATGAGCATTT GTCCACATAT ACAGCAAGTA TTTCAGAATG AAAAGTCTAA AGATGGGGTT 60
CTAAAAACGT GCAATGCTGC CAGGTATATA TTAAATCATT CCGTACCCAA GGAAAAATTC 120

It may take some time, please wait.

Sequence Source

Ensembl

Keyword

KW-0002--3D-structure
KW-0181--Complete proteome
KW-0378--Hydrolase
KW-0479--Metal-binding
KW-0539--Nucleus
KW-0645--Protease
KW-1185--Reference proteome
KW-0788--Thiol protease
KW-0804--Transcription
KW-0805--Transcription regulation
KW-0833--Ubl conjugation pathway
KW-0862--Zinc
KW-0863--Zinc-finger

Interpro

IPR001394--Peptidase_C19_UCH
IPR018200--USP_CS
IPR028889--USP_dom
IPR013083--Znf_RING/FYVE/PHD
IPR001607--Znf_UBP

PROSITE

PS00972--USP_1
PS00973--USP_2
PS50235--USP_3
PS50271--ZF_UBP

Pfam

PF00443--UCH
PF02148--zf-UBP

SMART

SM00290--ZnF_UBP

Gene Ontology

GO:0071819--C:DUBm complex
GO:0000124--C:SAGA complex
GO:0046695--C:SLIK (SAGA-like) complex
GO:0032947--F:protein complex scaffold
GO:0004843--F:thiol-dependent ubiquitin-specific protease activity
GO:0008270--F:zinc ion binding
GO:0016578--P:histone deubiquitination
GO:0051568--P:histone H3-K4 methylation
GO:0034729--P:histone H3-K79 methylation
GO:0006355--P:regulation of transcription, DNA-templated
GO:0008380--P:RNA splicing
GO:0006351--P:transcription, DNA-templated
GO:0006511--P:ubiquitin-dependent protein catabolic process

KEGG

sce:YMR223W

Orthology

iUUCD ID	Species	Identity	E-value	Score
IUUC-Ata-001055	Aegilops tauschii	30.36	4.00e-37	148.00
IUUC-Aml-001343	Ailuropoda melanoleuca	32.47	2.00e-56	211.00
IUUC-Atr-002653	Amborella trichopoda	28.39	3.00e-50	191.00
IUUC-Apl-003433	Anas platyrhynchos	31.03	4.00e-55	206.00
IUUC-Aca-005347	Anolis carolinensis	30.28	3.00e-54	204.00
IUUC-Aly-006565	Arabidopsis lyrata	28.89	6.00e-40	156.00
IUUC-Ath-007536	Arabidopsis thaliana	29.52	3.00e-40	157.00
IUUC-Ago-007811	Ashbya gossypii	50.52	2.00e-149	520.00
IUUC-Acl-008124	Aspergillus clavatus	33.95	3.00e-59	220.00
IUUC-Afl-008464	Aspergillus flavus	35.67	9.00e-52	195.00
IUUC-Afu-008912	Aspergillus fumigatus	33.11	2.00e-60	224.00
IUUC-Ani-009168	Aspergillus nidulans	33.63	6.00e-58	216.00
IUUC-Ang-009694	Aspergillus niger	31.32	4.00e-57	213.00
IUUC-Aor-010035	Aspergillus oryzae	39.37	2.00e-44	170.00
IUUC-Ate-010382	Aspergillus terreus	36.77	9.00e-55	205.00
IUUC-Ame-011253	Astyanax mexicanus	30.24	7.00e-47	179.00
IUUC-Bgr-012150	Blumeria graminis	30.99	9.00e-51	192.00
IUUC-Bta-013303	Bos taurus	31.60	1.00e-56	211.00
IUUC-Bci-013604	Botrytis cinerea	30.43	3.00e-56	210.00
IUUC-Bdi-014171	Brachypodium distachyon	28.98	8.00e-41	159.00
IUUC-Bol-016509	Brassica oleracea	28.45	3.00e-44	171.00
IUUC-Bra-016962	Brassica rapa	28.17	6.00e-45	172.00
IUUC-Cel-018186	Caenorhabditis elegans	30.53	8.00e-34	136.00
IUUC-Cja-019283	Callithrix jacchus	30.96	7.00e-51	192.00
IUUC-Cfa-021239	Canis familiaris	31.82	3.00e-57	213.00
IUUC-Cpo-022354	Cavia porcellus	31.83	7.00e-57	213.00
IUUC-Csa-023145	Chlorocebus sabaeus	31.39	3.00e-56	210.00
IUUC-Cho-024863	Choloepus hoffmanni	34.88	4.00e-25	107.00
IUUC-Csv-026214	Ciona savignyi	27.10	8.00e-52	196.00
IUUC-Cgl-026457	Colletotrichum gloeosporioides	30.95	6.00e-57	213.00
IUUC-Cne-027085	Cryptococcus neoformans	28.35	1.00e-39	155.00
IUUC-Cme-027339	Cyanidioschyzon merolae	28.91	3.00e-38	150.00
IUUC-Dre-027433	Danio rerio	30.80	8.00e-54	202.00
IUUC-Dno-030095	Dasypus novemcinctus	31.17	3.00e-56	210.00
IUUC-Dse-031415	Dothistroma septosporum	31.09	1.00e-67	248.00
IUUC-Dme-032074	Drosophila melanogaster	29.69	6.00e-53	199.00
IUUC-Ete-033088	Echinops telfairi	29.91	4.00e-33	135.00
IUUC-Eca-033736	Equus caballus	31.60	5.00e-57	213.00
IUUC-Eeu-035268	Erinaceus europaeus	30.71	1.00e-23	102.00
IUUC-Fca-035861	Felis catus	31.60	6.00e-57	213.00
IUUC-Fal-037645	Ficedula albicollis	31.03	3.00e-55	207.00
IUUC-Fox-038046	Fusarium oxysporum	31.43	1.00e-54	205.00
IUUC-Fso-038321	Fusarium solani	31.16	2.00e-50	191.00
IUUC-Gmo-039033	Gadus morhua	31.42	2.00e-39	155.00
IUUC-Ggr-040044	Gaeumannomyces graminis	30.85	1.00e-54	205.00
IUUC-Gga-040624	Gallus gallus	31.03	3.00e-55	207.00
IUUC-Gac-042197	Gasterosteus aculeatus	29.51	9.00e-50	189.00
IUUC-Gma-043933	Glycine max	30.12	1.00e-50	192.00
IUUC-Ggo-044409	Gorilla gorilla	31.39	2.00e-56	211.00
IUUC-Hsa-046521	Homo sapiens	31.39	2.00e-56	211.00
IUUC-Hvu-047739	Hordeum vulgare	28.88	5.00e-40	155.00
IUUC-Itr-048375	Ictidomys tridecemlineatus	31.60	4.00e-57	213.00
IUUC-Kpa-049135	Komagataella pastoris	37.03	7.00e-88	315.00
IUUC-Lch-050537	Latimeria chalumnae	31.82	9.00e-57	212.00
IUUC-Lpe-050969	Leersia perrieri	29.72	3.00e-39	154.00
IUUC-Loc-052765	Lepisosteus oculatus	27.82	1.00e-43	168.00
IUUC-Lma-053105	Leptosphaeria maculans	32.52	3.00e-61	227.00
IUUC-Laf-053571	Loxodonta africana	31.39	1.00e-56	211.00
IUUC-Mcc-055166	Macaca mulatta	31.39	3.00e-56	210.00
IUUC-Meu-056697	Macropus eugenii	31.12	2.00e-35	142.00
IUUC-Mor-057103	Magnaporthe oryzae	30.50	2.00e-53	201.00
IUUC-Mpo-057621	Magnaporthe poae	30.30	3.00e-55	207.00
IUUC-Mtr-057894	Medicago truncatula	34.34	2.00e-52	198.00
IUUC-Mla-059185	Melampsora laricipopulina	31.22	2.00e-48	184.00
IUUC-Mga-059709	Meleagris gallopavo	31.03	4.00e-55	206.00
IUUC-Mvi-060530	Microbotryum violaceum	32.43	6.00e-51	192.00
IUUC-Mmr-060988	Microcebus murinus	31.39	2.00e-56	211.00
IUUC-Mdo-063065	Monodelphis domestica	32.03	2.00e-56	211.00
IUUC-Mmu-063829	Mus musculus	31.60	1.00e-56	211.00
IUUC-Mac-065419	Musa acuminata	31.98	5.00e-44	170.00
IUUC-Mpu-066687	Mustela putorius furo	31.17	1.00e-55	208.00
IUUC-Mlu-067330	Myotis lucifugus	31.08	7.00e-55	206.00
IUUC-Nfi-068423	Neosartorya fischeri	33.96	4.00e-60	223.00
IUUC-Ncr-068809	Neurospora crassa	29.30	2.00e-49	187.00
IUUC-Nle-069859	Nomascus leucogenys	29.54	5.00e-54	203.00
IUUC-Ont-071961	Oreochromis niloticus	30.59	4.00e-50	190.00
IUUC-Oan-073565	Ornithorhynchus anatinus	29.16	6.00e-53	199.00
IUUC-Ocu-074951	Oryctolagus cuniculus	30.87	1.00e-54	205.00
IUUC-Oba-075688	Oryza barthii	29.53	2.00e-39	154.00
IUUC-Obr-076652	Oryza brachyantha	29.53	8.00e-40	155.00
IUUC-Ogl-077910	Oryza glaberrima	29.53	2.00e-39	155.00
IUUC-Ogu-078479	Oryza glumaepatula	29.53	2.00e-39	155.00
IUUC-Oin-079697	Oryza indica	29.27	4.00e-39	153.00
IUUC-Olo-080569	Oryza longistaminata	31.56	7.00e-38	150.00
IUUC-Ome-081706	Oryza meridionalis	29.53	3.00e-39	154.00
IUUC-Oni-083070	Oryza nivara	29.27	3.00e-39	154.00
IUUC-Opu-083249	Oryza punctata	28.70	1.00e-35	142.00
IUUC-Oru-084522	Oryza rufipogon	29.53	2.00e-39	155.00
IUUC-Osa-085351	Oryza sativa	29.27	7.00e-39	153.00
IUUC-Ola-086743	Oryzias latipes	33.88	8.00e-50	188.00
IUUC-Olu-087695	Ostreococcus lucimarinus	32.15	2.00e-40	157.00
IUUC-Oga-089131	Otolemur garnettii	30.96	3.00e-55	207.00
IUUC-Oar-089319	Ovis aries	31.60	1.00e-56	211.00
IUUC-Ptr-090783	Pan troglodytes	31.39	2.00e-56	211.00
IUUC-Pan-092927	Papio anubis	31.39	3.00e-56	210.00
IUUC-Psi-093670	Pelodiscus sinensis	31.03	4.00e-55	206.00
IUUC-Pma-094323	Petromyzon marinus	27.14	5.00e-44	169.00
IUUC-Pno-095141	Phaeosphaeria nodorum	32.01	8.00e-54	202.00
IUUC-Ppa-095413	Physcomitrella patens	30.32	2.00e-45	175.00
IUUC-Pfo-096462	Poecilia formosa	31.60	5.00e-55	206.00
IUUC-Pab-097612	Pongo abelii	31.39	2.00e-56	211.00
IUUC-Pop-099893	Populus trichocarpa	29.51	8.00e-53	199.00
IUUC-Pca-100329	Procavia capensis	31.08	7.00e-55	206.00
IUUC-Ppe-101583	Prunus persica	28.79	2.00e-44	171.00
IUUC-Pva-102409	Pteropus vampyrus	33.69	3.00e-38	150.00
IUUC-Pgr-103657	Puccinia graminis	32.09	6.00e-44	169.00
IUUC-Ptt-103887	Puccinia triticina	30.47	1.00e-35	142.00
IUUC-Pte-104340	Pyrenophora teres	31.49	3.00e-56	210.00
IUUC-Pyt-104782	Pyrenophora triticirepentis	32.99	1.00e-62	231.00
IUUC-Rno-105247	Rattus norvegicus	31.60	1.00e-56	211.00
IUUC-Sha-107019	Sarcophilus harrisii	31.72	7.00e-36	144.00
IUUC-Sja-107656	Schizosaccharomyces japonicus	32.66	3.00e-60	223.00
IUUC-Spo-108226	Schizosaccharomyces pombe	33.48	1.00e-63	235.00
IUUC-Ssl-108531	Sclerotinia sclerotiorum	29.03	1.00e-52	198.00
IUUC-Smo-109310	Selaginella moellendorffii	30.16	2.00e-54	204.00
IUUC-Sit-109716	Setaria italica	29.46	5.00e-39	153.00
IUUC-Sly-111077	Solanum lycopersicum	29.86	1.00e-47	181.00
IUUC-Stu-112203	Solanum tuberosum	31.81	3.00e-45	174.00
IUUC-Sar-113174	Sorex araneus	29.80	2.00e-44	171.00
IUUC-Sbi-114205	Sorghum bicolor	29.72	4.00e-39	154.00
IUUC-Sre-115195	Sporisorium reilianum	24.10	4.00e-40	157.00
IUUC-Ssc-115500	Sus scrofa	30.53	7.00e-55	206.00
IUUC-Tgu-116938	Taeniopygia guttata	32.03	1.00e-56	211.00
IUUC-Tru-117622	Takifugu rubripes	30.67	3.00e-53	200.00
IUUC-Tsy-119413	Tarsius syrichta	29.32	6.00e-54	203.00
IUUC-Tni-120119	Tetraodon nigroviridis	31.39	4.00e-55	207.00
IUUC-Tca-121154	Theobroma cacao	27.99	2.00e-50	191.00
IUUC-Tre-122139	Trichoderma reesei	31.09	9.00e-51	192.00
IUUC-Tvi-122599	Trichoderma virens	30.20	1.00e-51	195.00
IUUC-Tae-125608	Triticum aestivum	30.08	6.00e-45	173.00
IUUC-Tur-126423	Triticum urartu	30.36	4.00e-37	148.00
IUUC-Tme-127115	Tuber melanosporum	35.97	5.00e-70	256.00
IUUC-Ttr-129006	Tursiops truncatus	30.70	4.00e-53	200.00
IUUC-Uma-129455	Ustilago maydis	24.60	1.00e-44	172.00
IUUC-Vda-129829	Verticillium dahliae	31.92	2.00e-39	153.00
IUUC-Vvi-131477	Vitis vinifera	27.27	5.00e-39	153.00
IUUC-Xtr-132444	Xenopus tropicalis	30.69	3.00e-55	207.00
IUUC-Xma-133514	Xiphophorus maculatus	31.89	5.00e-55	206.00
IUUC-Yli-134357	Yarrowia lipolytica	31.57	2.00e-56	211.00
IUUC-Zma-134945	Zea mays	29.35	1.00e-39	155.00

Created Date

25-Jun-2017

Functional Description

Protein Fasta Sequence

Nucleotide Fasta Sequence