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P54728

- RD23B_MOUSE

UniProt

P54728 - RD23B_MOUSE

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Protein
UV excision repair protein RAD23 homolog B
Gene
Rad23b, Mhr23b
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Multiubiquitin chain receptor involved in modulation of proteasomal degradation. Binds to polyubiquitin chains. Proposed to be capable to bind simultaneously to the 26S proteasome and to polyubiquitinated substrates and to deliver ubiquitinated proteins to the proteasome. May play a role in endoplasmic reticulum-associated degradation (ERAD) of misfolded glycoproteins by association with PNGase and delivering deglycosylated proteins to the proteasome.3 Publications
Involved in global genome nucleotide excision repair (GG-NER) by acting as component of the XPC complex. Cooperatively with Cetn2 appears to stabilize Xpc. May protect Xpc from proteasomal degradation By similarity.3 Publications
The XPC complex is proposed to represent the first factor bound at the sites of DNA damage and together with other core recognition factors, Xpa, RPA and the TFIIH complex, is part of the pre-incision (or initial recognition) complex. The XPC complex recognizes a wide spectrum of damaged DNA characterized by distortions of the DNA helix such as single-stranded loops, mismatched bubbles or single-stranded overhangs. The orientation of XPC complex binding appears to be crucial for inducing a productive NER. XPC complex is proposed to recognize and to interact with unpaired bases on the undamaged DNA strand which is followed by recruitment of the TFIIH complex and subsequent scanning for lesions in the opposite strand in a 5'-to-3' direction by the NER machinery. Cyclobutane pyrimidine dimers (CPDs) which are formed upon UV-induced DNA damage esacpe detection by the XPC complex due to a low degree of structural perurbation. Instead they are detected by the UV-DDB complex which in turn recruits and cooperates with the XPC complex in the respective DNA repair. In vitro, the Xpc:Rad23b dimer is sufficient to initiate NER; it preferentially binds to cisplatin and UV-damaged double-stranded DNA and also binds to a variety of chemically and structurally diverse DNA adducts. Xpc:Rad23b contacts DNA both 5' and 3' of a cisplatin lesion with a preference for the 5' side. Xpc:Rad23bB induces a bend in DNA upon binding. Xpc:Rad23b stimulates the activity of DNA glycosylases Tdg and Smug1 By similarity.3 Publications

GO - Molecular functioni

  1. damaged DNA binding Source: InterPro
  2. protein binding Source: UniProtKB

GO - Biological processi

  1. cellular response to DNA damage stimulus Source: MGI
  2. nucleotide-excision repair, DNA damage recognition Source: Ensembl
  3. proteasome-mediated ubiquitin-dependent protein catabolic process Source: InterPro
  4. regulation of proteasomal ubiquitin-dependent protein catabolic process Source: Ensembl
  5. spermatogenesis Source: MGI
Complete GO annotation...

Keywords - Biological processi

DNA damage, DNA repair, Ubl conjugation pathway

Enzyme and pathway databases

ReactomeiREACT_210532. DNA Damage Recognition in GG-NER.

Names & Taxonomyi

Protein namesi
Recommended name:
UV excision repair protein RAD23 homolog B
Short name:
HR23B
Short name:
mHR23B
Alternative name(s):
XP-C repair-complementing complex 58 kDa protein
Short name:
p58
Gene namesi
Name:Rad23b
Synonyms:Mhr23b
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 4

Organism-specific databases

MGIiMGI:105128. Rad23b.

Subcellular locationi

Nucleus. Cytoplasm 1 Publication

GO - Cellular componenti

  1. XPC complex Source: UniProtKB
  2. cytoplasm Source: UniProtKB-SubCell
  3. proteasome complex Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Proteasome

Pathology & Biotechi

Disruption phenotypei

Impaired embryonic development with a 90 % rate of intrauterine or neonatal death. Surviving animals display a variety of abnormalities, including retarded growth, facial dysmorphology and male sterility. The effect on NER competence is reported conflictingly: According 1 Publication no change in NER activity is found and according 1 Publication a reduced NER activity is seen. Embryonic lethal with Rad23a and Rad23b double deficiency. Double deficient cells show reduced cell survival upopn UV radiation and reduced steady-state level of Xpc indicating a reduced NER capacity.3 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 416416UV excision repair protein RAD23 homolog B
PRO_0000114907Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei155 – 1551Phosphothreonine By similarity
Modified residuei160 – 1601Phosphoserine By similarity
Modified residuei174 – 1741Phosphoserine By similarity
Modified residuei186 – 1861Phosphothreonine By similarity
Modified residuei199 – 1991Phosphoserine By similarity
Modified residuei202 – 2021Phosphotyrosine By similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP54728.
PaxDbiP54728.
PRIDEiP54728.

PTM databases

PhosphoSiteiP54728.

Expressioni

Gene expression databases

ArrayExpressiP54728.
BgeeiP54728.
CleanExiMM_RAD23B.
GenevestigatoriP54728.

Interactioni

Subunit structurei

Component of the XPC complex composed of XPC, RAD23B and CETN2. Interacts with NGLY1 and PSMC1. Interacts with ATXN3 By similarity. Interacts with AMFR. Interacts with VCP; the interaction is indirect and mediated by NGLY1.4 Publications

Protein-protein interaction databases

BioGridi202562. 7 interactions.
IntActiP54728. 8 interactions.
MINTiMINT-214731.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi275 – 2795
Helixi283 – 29412
Helixi296 – 2983
Helixi299 – 30911
Helixi311 – 3199
Helixi321 – 3288

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2F4MX-ray1.85B273-332[»]
2F4OX-ray2.26B273-332[»]
ProteinModelPortaliP54728.
SMRiP54728. Positions 1-416.

Miscellaneous databases

EvolutionaryTraceiP54728.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 7979Ubiquitin-like
Add
BLAST
Domaini188 – 22841UBA 1
Add
BLAST
Domaini274 – 31744STI1
Add
BLAST
Domaini371 – 41141UBA 2
Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi255 – 2617Poly-Ala
Compositional biasi262 – 2709Poly-Thr
Compositional biasi336 – 35520Poly-Gly
Add
BLAST

Sequence similaritiesi

Belongs to the RAD23 family.
Contains 1 STI1 domain.
Contains 2 UBA domains.

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG5272.
GeneTreeiENSGT00390000012078.
HOGENOMiHOG000172162.
HOVERGENiHBG055042.
InParanoidiQ3TUA4.
KOiK10839.
OMAiQQKFVIE.
OrthoDBiEOG72C51D.
TreeFamiTF101216.

Family and domain databases

Gene3Di1.10.10.540. 1 hit.
InterProiIPR004806. Rad23.
IPR006636. STI1_HS-bd.
IPR009060. UBA-like.
IPR015940. UBA/transl_elong_EF1B_N_euk.
IPR000449. UBA/Ts_N.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR015360. XPC-bd.
[Graphical view]
PfamiPF00627. UBA. 2 hits.
PF00240. ubiquitin. 1 hit.
PF09280. XPC-binding. 1 hit.
[Graphical view]
PRINTSiPR01839. RAD23PROTEIN.
SMARTiSM00727. STI1. 1 hit.
SM00165. UBA. 2 hits.
SM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF101238. SSF101238. 1 hit.
SSF46934. SSF46934. 2 hits.
SSF54236. SSF54236. 1 hit.
TIGRFAMsiTIGR00601. rad23. 1 hit.
PROSITEiPS50030. UBA. 2 hits.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P54728-1 [UniParc]FASTAAdd to Basket

« Hide

MQVTLKTLQQ QTFKIDIDPE ETVKALKEKI ESEKGKDAFP VAGQKLIYAG    50
KILSDDTALK EYKIDEKNFV VVMVTKPKAV TTAVPATTQP SSTPSPTAVS 100
SSPAVAAAQA PAPTPALPPT STPASTAPAS TTASSEPAPA GATQPEKPAE 150
KPAQTPVLTS PAPADSTPGD SSRSNLFEDA TSALVTGQSY ENMVTEIMSM 200
GYEREQVIAA LRASFNNPDR AVEYLLMGIP GDRESQAVVD PPPQAVSTGT 250
PQSPAVAAAA ATTTATTTTT SGGHPLEFLR NQPQFQQMRQ IIQQNPSLLP 300
ALLQQIGREN PQLLQQISQH QEHFIQMLNE PVQEAGSQGG GGGGGGGGGG 350
GGGGGIAEAG SGHMNYIQVT PQEKEAIERL KALGFPEGLV IQAYFACEKN 400
ENLAANFLLQ QNFDED 416
Length:416
Mass (Da):43,513
Last modified:July 27, 2011 - v2
Checksum:i7440E6A9C8ADF454
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti98 – 981A → T in CAA63146. 1 Publication
Sequence conflicti98 – 981A → T in AAH27747. 1 Publication
Sequence conflicti118 – 1181P → A in CAA63146. 1 Publication
Sequence conflicti118 – 1181P → A in AAH27747. 1 Publication
Sequence conflicti127 – 1271A → T in CAA63146. 1 Publication
Sequence conflicti127 – 1271A → T in AAH27747. 1 Publication
Sequence conflicti337 – 3371S → G in CAA63146. 1 Publication
Sequence conflicti337 – 3371S → G in AAH27747. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X92411 mRNA. Translation: CAA63146.1.
AK150089 mRNA. Translation: BAE29298.1.
AK160880 mRNA. Translation: BAE36067.1.
AK160890 mRNA. Translation: BAE36071.1.
AK160973 mRNA. Translation: BAE36124.1.
AL683890 Genomic DNA. Translation: CAM13976.1.
BC027747 mRNA. Translation: AAH27747.1.
CCDSiCCDS18194.1.
RefSeqiNP_033037.2. NM_009011.4.
UniGeneiMm.196846.

Genome annotation databases

EnsembliENSMUST00000030134; ENSMUSP00000030134; ENSMUSG00000028426.
GeneIDi19359.
KEGGimmu:19359.
UCSCiuc012dej.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X92411 mRNA. Translation: CAA63146.1 .
AK150089 mRNA. Translation: BAE29298.1 .
AK160880 mRNA. Translation: BAE36067.1 .
AK160890 mRNA. Translation: BAE36071.1 .
AK160973 mRNA. Translation: BAE36124.1 .
AL683890 Genomic DNA. Translation: CAM13976.1 .
BC027747 mRNA. Translation: AAH27747.1 .
CCDSi CCDS18194.1.
RefSeqi NP_033037.2. NM_009011.4.
UniGenei Mm.196846.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2F4M X-ray 1.85 B 273-332 [» ]
2F4O X-ray 2.26 B 273-332 [» ]
ProteinModelPortali P54728.
SMRi P54728. Positions 1-416.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 202562. 7 interactions.
IntActi P54728. 8 interactions.
MINTi MINT-214731.

PTM databases

PhosphoSitei P54728.

Proteomic databases

MaxQBi P54728.
PaxDbi P54728.
PRIDEi P54728.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000030134 ; ENSMUSP00000030134 ; ENSMUSG00000028426 .
GeneIDi 19359.
KEGGi mmu:19359.
UCSCi uc012dej.1. mouse.

Organism-specific databases

CTDi 5887.
MGIi MGI:105128. Rad23b.

Phylogenomic databases

eggNOGi COG5272.
GeneTreei ENSGT00390000012078.
HOGENOMi HOG000172162.
HOVERGENi HBG055042.
InParanoidi Q3TUA4.
KOi K10839.
OMAi QQKFVIE.
OrthoDBi EOG72C51D.
TreeFami TF101216.

Enzyme and pathway databases

Reactomei REACT_210532. DNA Damage Recognition in GG-NER.

Miscellaneous databases

ChiTaRSi RAD23B. mouse.
EvolutionaryTracei P54728.
NextBioi 296413.
PROi P54728.
SOURCEi Search...

Gene expression databases

ArrayExpressi P54728.
Bgeei P54728.
CleanExi MM_RAD23B.
Genevestigatori P54728.

Family and domain databases

Gene3Di 1.10.10.540. 1 hit.
InterProi IPR004806. Rad23.
IPR006636. STI1_HS-bd.
IPR009060. UBA-like.
IPR015940. UBA/transl_elong_EF1B_N_euk.
IPR000449. UBA/Ts_N.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR015360. XPC-bd.
[Graphical view ]
Pfami PF00627. UBA. 2 hits.
PF00240. ubiquitin. 1 hit.
PF09280. XPC-binding. 1 hit.
[Graphical view ]
PRINTSi PR01839. RAD23PROTEIN.
SMARTi SM00727. STI1. 1 hit.
SM00165. UBA. 2 hits.
SM00213. UBQ. 1 hit.
[Graphical view ]
SUPFAMi SSF101238. SSF101238. 1 hit.
SSF46934. SSF46934. 2 hits.
SSF54236. SSF54236. 1 hit.
TIGRFAMsi TIGR00601. rad23. 1 hit.
PROSITEi PS50030. UBA. 2 hits.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning, comparative mapping, and RNA expression of the mouse homologues of the Saccharomyces cerevisiae nucleotide excision repair gene RAD23."
    van der Spek P.J., Visser C.E., Hanaoka F., Smit B., Hagemeijer A., Bootsma D., Hoeijmakers J.H.J.
    Genomics 31:20-27(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: BALB/c.
    Tissue: Testis.
  2. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Bone marrow, Embryo and Head.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: FVB/N.
    Tissue: Mammary gland.
  5. "Identification of proteins that interact with mammalian peptide:N-glycanase and implicate this hydrolase in the proteasome-dependent pathway for protein degradation."
    Park H., Suzuki T., Lennarz W.J.
    Proc. Natl. Acad. Sci. U.S.A. 98:11163-11168(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH NGLY1.
  6. Cited for: DISRUPTION PHENOTYPE.
  7. "A novel regulation mechanism of DNA repair by damage-induced and RAD23-dependent stabilization of xeroderma pigmentosum group C protein."
    Ng J.M., Vermeulen W., van der Horst G.T., Bergink S., Sugasawa K., Vrieling H., Hoeijmakers J.H.
    Genes Dev. 17:1630-1645(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.
  8. "Relative levels of the two mammalian Rad23 homologs determine composition and stability of the xeroderma pigmentosum group C protein complex."
    Okuda Y., Nishi R., Ng J.M., Vermeulen W., van der Horst G.T., Mori T., Hoeijmakers J.H., Hanaoka F., Sugasawa K.
    DNA Repair 3:1285-1295(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE.
  9. "A complex between peptide:N-glycanase and two proteasome-linked proteins suggests a mechanism for the degradation of misfolded glycoproteins."
    Katiyar S., Li G., Lennarz W.J.
    Proc. Natl. Acad. Sci. U.S.A. 101:13774-13779(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH NGLY1.
  10. "Multiple modes of interaction of the deglycosylation enzyme, mouse peptide N-glycanase, with the proteasome."
    Li G., Zhou X., Zhao G., Schindelin H., Lennarz W.J.
    Proc. Natl. Acad. Sci. U.S.A. 102:15809-15814(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH NGLY1.
  11. Erratum
    Li G., Zhou X., Zhao G., Schindelin H., Lennarz W.J.
    Proc. Natl. Acad. Sci. U.S.A. 103:1153-1153(2006)
  12. "The AAA ATPase p97 links peptide N-glycanase to the endoplasmic reticulum-associated E3 ligase autocrine motility factor receptor."
    Li G., Zhao G., Zhou X., Schindelin H., Lennarz W.J.
    Proc. Natl. Acad. Sci. U.S.A. 103:8348-8353(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN ERAD, INTERACTION WITH AMFR; NGLY1 AND DEGLYCOSYLATED PROTEINS.
  13. "Structure of the mouse peptide N-glycanase-HR23 complex suggests co-evolution of the endoplasmic reticulum-associated degradation and DNA repair pathways."
    Zhao G., Zhou X., Wang L., Li G., Kisker C., Lennarz W.J., Schindelin H.
    J. Biol. Chem. 281:13751-13761(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 273-332 IN COMPLEX WITH NGLY1.

Entry informationi

Entry nameiRD23B_MOUSE
AccessioniPrimary (citable) accession number: P54728
Secondary accession number(s): Q3TUA4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: July 27, 2011
Last modified: September 3, 2014
This is version 125 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi