P55036 (PSMD4_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
26S proteasome non-ATPase regulatory subunit 4

Alternative name(s):
26S proteasome regulatory subunit RPN10
26S proteasome regulatory subunit S5A
Antisecretory factor 1
Short name=AF
Short name=ASF
Multiubiquitin chain-binding protein

Gene names

Name:	PSMD4
Synonyms:	MCB1

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	377 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Binds and presumably selects ubiquitin-conjugates for destruction. Displays selectivity for longer polyubiquitin chains. Modulates intestinal fluid secretion.
Subunit structure	The 26S proteasome is composed of a core protease, known as the 20S proteasome, capped at one or both ends by the 19S regulatory complex (RC). The RC is composed of at least 18 different subunits in two subcomplexes, the base and the lid, which form the portions proximal and distal to the 20S proteolytic core, respectively. Directly interacts with NUB1. Interacts with SQSTM1. Ref.11 Ref.13
Domain	The 2 UIM motifs are involved in the binding to a multi-ubiquitin chain in a cooperative way. Ref.19 Ref.20
Post-translational modification	Phosphorylated upon DNA damage, probably by ATM or ATR. Ref.14 Ref.15 Ref.16 Ref.17
Sequence similarities	Belongs to the proteasome subunit S5A family. Contains 2 UIM (ubiquitin-interacting motif) repeats. Contains 1 VWFA domain.

Ontologies

Keywords
Cellular component	Proteasome
Coding sequence diversity	Alternative splicing
Domain	Repeat
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest Traceable author statement. Source: Reactome DNA repair Inferred from electronic annotation. Source: InterPro G1/S transition of mitotic cell cycle Traceable author statement. Source: Reactome M/G1 transition of mitotic cell cycle Traceable author statement. Source: Reactome S phase of mitotic cell cycle Traceable author statement. Source: Reactome anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process Traceable author statement. Source: Reactome antigen processing and presentation of peptide antigen via MHC class I Traceable author statement. Source: Reactome apoptotic process Traceable author statement. Source: Reactome mRNA metabolic process Traceable author statement. Source: Reactome negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle Traceable author statement. Source: Reactome positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle Traceable author statement. Source: Reactome protein polyubiquitination Traceable author statement. Source: Reactome regulation of apoptotic process Traceable author statement. Source: Reactome regulation of cellular amino acid metabolic process Traceable author statement. Source: Reactome regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro viral reproduction Traceable author statement. Source: Reactome
Cellular component	cytosol Traceable author statement. Source: Reactome nucleoplasm Traceable author statement. Source: Reactome proteasome complex Traceable author statement. Source: ProtInc
Molecular function	protein binding Inferred from physical interaction. Source: IntAct zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
Pax3	P24610	3	EBI-359318,EBI-1208116	From a different organism.
RAD23A	P54725	2	EBI-359318,EBI-746453
RAD23B	P54727	5	EBI-359318,EBI-954531
SCHIP1	Q9P0W5	2	EBI-359318,EBI-1397509

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Note: Additional isoforms seem to exist.

Isoform Rpn10A (identifier: P55036-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform Rpn10E (identifier: P55036-2)

The sequence of this isoform differs from the canonical sequence as follows:
     255-268: DSDDALLKMTISQQ → GERGGIRSPGTAGC
     269-377: Missing.

Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.14

Chain

2 – 377

376

26S proteasome non-ATPase regulatory subunit 4

PRO_0000173828

Regions

Domain

5 – 188

184

VWFA

Repeat

211 – 230

20

UIM 1

Repeat

282 – 301

20

UIM 2

Region

216 – 220

5

Essential for ubiquitin-binding

Region

287 – 291

5

Essential for ubiquitin-binding

Compositional bias

238 – 246

9

Poly-Ala

Amino acid modifications

Modified residue

250

1

Phosphothreonine By similarity

Modified residue

256

1

Phosphoserine By similarity

Modified residue

266

1

Phosphoserine Ref.14 Ref.15 Ref.16 Ref.17

Modified residue

358

1

Phosphoserine Ref.14

Modified residue

361

1

Phosphoserine Ref.14

Natural variations

Alternative sequence

255 – 268

14

DSDDA…TISQQ → GERGGIRSPGTAGC in isoform Rpn10E.

VSP_005291

Alternative sequence

269 – 377

109

Missing in isoform Rpn10E.

VSP_005292

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

377

Helix Strand Turn

Details...

Beta strand

201 – 203

3

Helix

210 – 212

3

Helix

214 – 244

31

Beta strand

245 – 249

5

Helix

257 – 272

16

Beta strand

273 – 275

3

Helix

278 – 294

17

Beta strand

296 – 300

5

Sequences

	Sequence		Length	Mass (Da)
	Isoform Rpn10A [UniParc]. Last modified October 1, 1996. Version 1. Checksum: EC712EC4DB1CE9AB	FASTA	377	40,737
	10 20 30 40 50 60 MVLESTMVCV DNSEYMRNGD FLPTRLQAQQ DAVNIVCHSK TRSNPENNVG LITLANDCEV 70 80 90 100 110 120 LTTLTPDTGR ILSKLHTVQP KGKITFCTGI RVAHLALKHR QGKNHKMRII AFVGSPVEDN 130 140 150 160 170 180 EKDLVKLAKR LKKEKVNVDI INFGEEEVNT EKLTAFVNTL NGKDGTGSHL VTVPPGPSLA 190 200 210 220 230 240 DALISSPILA GEGGAMLGLG ASDFEFGVDP SADPELALAL RVSMEEQRQR QEEEARRAAA 250 260 270 280 290 300 ASAAEAGIAT TGTEDSDDAL LKMTISQQEF GRTGLPDLSS MTEEEQIAYA MQMSLQGAEF 310 320 330 340 350 360 GQAESADIDA SSAMDTSEPA KEEDDYDVMQ DPEFLQSVLE NLPGVDPNNE AIRNAMGSLA 370 SQATKDGKKD KKEEDKK
	Isoform Rpn10E [UniParc]. Checksum: 6640BF4CD5C91C6E	FASTA	268	28,612
	10 20 30 40 50 60 MVLESTMVCV DNSEYMRNGD FLPTRLQAQQ DAVNIVCHSK TRSNPENNVG LITLANDCEV 70 80 90 100 110 120 LTTLTPDTGR ILSKLHTVQP KGKITFCTGI RVAHLALKHR QGKNHKMRII AFVGSPVEDN 130 140 150 160 170 180 EKDLVKLAKR LKKEKVNVDI INFGEEEVNT EKLTAFVNTL NGKDGTGSHL VTVPPGPSLA 190 200 210 220 230 240 DALISSPILA GEGGAMLGLG ASDFEFGVDP SADPELALAL RVSMEEQRQR QEEEARRAAA 250 260 ASAAEAGIAT TGTEGERGGI RSPGTAGC

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular cloning and expression of a pituitary gland protein modulating intestinal fluid secretion." Johansson E., Loennroth I., Lange S., Jonson I., Jennische E., Loennroth C. J. Biol. Chem. 270:20615-20620(1995) [PubMed: 7657640] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 63-75 AND 130-140. Tissue: Pituitary.
[2]	Loennroth I. Submitted (MAY-1997) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION.
[3]	"Molecular cloning and expression of a multiubiquitin chain binding subunit of the human 26S protease." Ferrell K., Deveraux Q., van Nocker S., Rechsteiner M. FEBS Lett. 381:143-148(1996) [PubMed: 8641424] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE.
[4]	"Developmentally regulated, alternative splicing of the Rpn10 gene generates multiple forms of 26S proteasomes." Kawahara H., Kasahara M., Nishiyama A., Ohsumi K., Goto T., Kishimoto T., Saeki Y., Yokosawa H., Shimbara N., Murata S., Chiba T., Suzuki K., Tanaka K. EMBO J. 19:4144-4153(2000) [PubMed: 10921894] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], ALTERNATIVE SPLICING. Tissue: Fetal brain.
[5]	"The DNA sequence and biological annotation of human chromosome 1." Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R. Nature 441:315-321(2006) [PubMed: 16710414] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Liver and Lung.
[8]	"Proteolysis of presenilin 1 is associated with the 26S proteasome and is altered in Alzheimer's disease." Fraser P.E., Levesque G., Rogaeva E.A., Yu G., St George-Hyslop P.H. Submitted (SEP-1996) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 70-377. Tissue: Brain.
[9]	"Purification and characterization of the antisecretory factor: a protein in the central nervous system and in the gut which inhibits intestinal hypersecretion induced by cholera toxin." Loennroth I., Lange S. Biochim. Biophys. Acta 883:138-144(1986) [PubMed: 3524692] [Abstract] Cited for: CHARACTERIZATION.
[10]	"Characterization of two polyubiquitin binding sites in the 26 S protease subunit 5a." Young P., Deveraux Q., Beal R.E., Pickart C.M., Rechsteiner M. J. Biol. Chem. 273:5461-5467(1998) [PubMed: 9488668] [Abstract] Cited for: POLYUBIQUITIN BINDING SITES.
[11]	"Targeting of NEDD8 and its conjugates for proteasomal degradation by NUB1." Kamitani T., Kito K., Fukuda-Kamitani T., Yeh E.T.H. J. Biol. Chem. 276:46655-46660(2001) [PubMed: 11585840] [Abstract] Cited for: INTERACTION WITH NUB1.
[12]	"An unappreciated role for RNA surveillance." Hillman R.T., Green R.E., Brenner S.E. Genome Biol. 5:R8.1-R8.16(2004) [PubMed: 14759258] [Abstract] Cited for: SPLICE ISOFORM(S) THAT ARE POTENTIAL NMD TARGET(S).
[13]	"Sequestosome 1/p62 is a polyubiquitin chain binding protein involved in ubiquitin proteasome degradation." Seibenhener M.L., Babu J.R., Geetha T., Wong H.C., Krishna N.R., Wooten M.W. Mol. Cell. Biol. 24:8055-8068(2004) [PubMed: 15340068] [Abstract] Cited for: INTERACTION WITH SQSTM1.
[14]	"Mass spectrometric characterization of the affinity-purified human 26S proteasome complex." Wang X., Chen C.-F., Baker P.R., Chen P.-L., Kaiser P., Huang L. Biochemistry 46:3553-3565(2007) [PubMed: 17323924] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-266; SER-358 AND SER-361, CLEAVAGE OF INITIATOR METHIONINE, MASS SPECTROMETRY. Tissue: Embryonic kidney.
[15]	"ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage." Matsuoka S., Ballif B.A., Smogorzewska A., McDonald E.R. III, Hurov K.E., Luo J., Bakalarski C.E., Zhao Z., Solimini N., Lerenthal Y., Shiloh Y., Gygi S.P., Elledge S.J. Science 316:1160-1166(2007) [PubMed: 17525332] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-266, MASS SPECTROMETRY. Tissue: Embryonic kidney.
[16]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-266, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[17]	"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed: 19690332] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-266, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[18]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed: 21269460] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[19]	"Structural determinants for the binding of ubiquitin-like domains to the proteasome." Mueller T.D., Feigon J. EMBO J. 22:4634-4645(2003) [PubMed: 12970176] [Abstract] Cited for: STRUCTURE BY NMR OF 263-306 IN COMPLEX WITH HR23A UBIQUITIN-LIKE DOMAIN.
[20]	"Structure of the ubiquitin-interacting motif of S5a bound to the ubiquitin-like domain of HR23B." Fujiwara K., Tenno T., Sugasawa K., Jee J.-G., Ohki I., Kojima C., Tochio H., Hiroaki H., Hanaoka F., Shirakawa M. J. Biol. Chem. 279:4760-4767(2004) [PubMed: 14585839] [Abstract] Cited for: STRUCTURE BY NMR OF 260-307 IN COMPLEX WITH HR23B UBIQUITIN-LIKE DOMAIN.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U51007 mRNA. Translation: AAC50433.1.
U24704 mRNA. Translation: AAB54057.1.
AB033605 mRNA. Translation: BAA97581.1.
AL391069, AL592424 Genomic DNA. Translation: CAH70329.1.
AL592424, AL391069 Genomic DNA. Translation: CAI16390.1.
CH471121 Genomic DNA. Translation: EAW53457.1.
CH471121 Genomic DNA. Translation: EAW53458.1.
BC002365 mRNA. Translation: AAH02365.1.
BC072008 mRNA. Translation: AAH72008.1.
U72664 mRNA. Translation: AAB68598.1.

IPI

IPI00022694.
IPI00216247.

PIR

S63671.

RefSeq

NP_002801.1. NM_002810.2.

UniGene

Hs.505059.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1P9C	NMR	-	A	263-307	[»]
1P9D	NMR	-	S	263-307	[»]
1UEL	NMR	-	B	263-307	[»]
1YX4	NMR	-	A	196-306	[»]
1YX5	NMR	-	A	196-306	[»]
1YX6	NMR	-	A	196-306	[»]
2KDE	NMR	-	A	196-306	[»]
2KDF	NMR	-	A	196-306	[»]

ProteinModelPortal

P55036.

SMR

P55036. Positions 196-306.

ModBase

Search...

Protein-protein interaction databases

IntAct

P55036. 20 interactions.

MINT

MINT-105366.

STRING

P55036.

PTM databases

PhosphoSite

P55036.

Polymorphism databases

DMDM

1709796.

Proteomic databases

PRIDE

P55036.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000368884; ENSP00000357879; ENSG00000159352.

GeneID

5710.

KEGG

hsa:5710.

NMPDR

fig|9606.3.peg.2018.

UCSC

uc001exl.1. human.

Organism-specific databases

CTD

5710.

GeneCards

GC01P151227.

H-InvDB

HIX0199945.

HGNC

HGNC:9561. PSMD4.

HPA

CAB047300.
HPA039252.

MIM

601648. gene.

neXtProt

NX_P55036.

PharmGKB

PA33907.

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG07297.

GeneTree

ENSGT00530000064050.

HOVERGEN

HBG000425.

OrthoDB

EOG4JQ3Z0.

PhylomeDB

P55036.

Enzyme and pathway databases

Reactome

REACT_111102. Signal Transduction.
REACT_111217. Metabolism.
REACT_13505. Proteasome mediated degradation of PAK-2p34.
REACT_152. Cell Cycle, Mitotic.
REACT_1538. Cell Cycle Checkpoints.
REACT_383. DNA Replication.
REACT_578. Apoptosis.
REACT_6185. HIV Infection.
REACT_6850. Cdc20:Phospho-APC/C mediated degradation of Cyclin A.
REACT_6900. Immune System.

Gene expression databases

ArrayExpress

P55036.

Bgee

P55036.

CleanEx

HS_PSMD4.

Genevestigator

P55036.

GermOnline

ENSG00000159352. Homo sapiens.

Family and domain databases

InterPro

IPR007198. Ssl1-like.
IPR003903. Ubiquitin-int_motif.
IPR002035. VWF_A.
[Graphical view]

KO

K03029.

Pfam

PF04056. Ssl1. 1 hit.
PF02809. UIM. 2 hits.
[Graphical view]

SMART

SM00726. UIM. 2 hits.
SM00327. VWA. 1 hit.
[Graphical view]

PROSITE

PS50330. UIM. 2 hits.
PS50234. VWFA. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

22186.

SOURCE

Search...

Entry information

Entry name

PSMD4_HUMAN

Accession

Primary (citable) accession number: P55036
Secondary accession number(s): D3DV16, Q5VWC5, Q9NS92

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	October 1, 1996
Last modified:	January 25, 2012
This is version 123 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.