Q17551 (RPM1_CAEEL) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
E3 ubiquitin-protein ligase rpm-1
EC=6.3.2.-

Alternative name(s):
Pam/highwire/rpm-1 protein
Regulator of presynaptic morphology protein 1
Synapse defective protein 3

Gene names

Name:	rpm-1
Synonyms:	syd-3
ORF Names:	C01B7.6

Organism

Caenorhabditis elegans [Reference proteome]

Taxonomic identifier

6239 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Protostomia › Ecdysozoa › Nematoda › Chromadorea › Rhabditida › Rhabditoidea › Rhabditidae › Peloderinae › Caenorhabditis

Protein attributes

Sequence length	3766 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins, including dlk-1. Negatively regulates a p38 MAP kinase pathway composed of dlk-1, mkk-4, and pmk-3 that functions presynaptically to regulate synaptic architecture. Has a role during synaptogenesis; regulates neuronal morphology, specifically presynaptic differentiation. May regulate the spatial arrangement of presynaptic terminals or restrict their development. Ref.1 Ref.2 Ref.5
Pathway	Protein modification; protein ubiquitination.
Subcellular location	Nucleus By similarity UniProtKB O75592.
Tissue specificity	Expression is seen in the pharynx, coelomocytes and distal tip cell. Most abundant expression is in axons of the nerve ring neuropil. Expression is not seen in body wall muscle, hypodermis or intestine. Ref.1 Ref.2
Developmental stage	First expressed in comma stage embryos and persists through to adulthood. Ref.2
Domain	The PHR domains are compact beta-sandwich folds composed of 11 antiparallel strands and decorated with conserved apical loops. They are likely to play a structural role and mediate interactions with substrates or partners By similarity.
Disruption phenotype	In mutants, mechanosensory neurons fail to accumulate tagged vesicles, retract synaptic branches and ectopically extend axons. Some motor neurons branch and overgrow, others show altered synaptic organization. Ref.2
Sequence similarities	Belongs to the highwire family. Contains 1 B box-type zinc finger. Contains 1 DOC domain. Contains 4 RCC1 repeats. Contains 1 RING-type zinc finger.

Ontologies

Keywords
Biological process	Transcription Transcription regulation Ubl conjugation pathway
Cellular component	Nucleus
Domain	Repeat Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Ligase
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	body morphogenesis Inferred from mutant phenotype Ref.2. Source: WormBase locomotion Inferred from genetic interaction Ref.5. Source: WormBase negative regulation of MAPK cascade Inferred from genetic interaction Ref.5. Source: WormBase oviposition Inferred from mutant phenotype Ref.2. Source: WormBase regulation of protein stability Inferred from mutant phenotype Ref.5. Source: WormBase regulation of synapse organization Inferred from mutant phenotype Ref.1Ref.2Ref.5. Source: WormBase regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	axon Inferred from direct assay Ref.2PubMed 17698012. Source: WormBase neuromuscular junction Inferred from direct assay Ref.1. Source: WormBase nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ubiquitin-protein ligase activity Inferred from direct assay Ref.5. Source: WormBase zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 3766	3766	E3 ubiquitin-protein ligase rpm-1		PRO_0000055970
Regions
	Repeat	631 – 682	52	RCC1 1
	Repeat	725 – 784	60	RCC1 2
	Repeat	785 – 836	52	RCC1 3
	Repeat	838 – 892	55	RCC1 4
	Domain	2870 – 3046	177	DOC
	Zinc finger	3331 – 3379	49	B box-type
	Zinc finger	3517 – 3568	52	RING-type; atypical
	Region	1056 – 1205	150	PHR domain 1 By similarity
	Region	1503 – 1655	153	PHR domain 2 By similarity
	Compositional bias	683 – 725	43	Cys-rich
	Compositional bias	2508 – 2538	31	Gly-rich
Experimental info
	Mutagenesis	3597	1	R → C in ky346; total number of the synaptic vesicle GFP puncta is reduced. Ref.1
	Mutagenesis	3675	1	C → Y in ju44; total number of the synaptic vesicle GFP puncta is reduced. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q17551 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: EAB59E816C5BBF4D	FASTA	3,766	418,058
	10 20 30 40 50 60 MSFFLREIDG ERVCSTSTET SIPEDRKSAR RLRKLLYKCA ENTCKPDILR VPAHCGKLDK 70 80 90 100 110 120 EEEKSKTPLD QQQQINFHDI LNSKFVVGPP SPFALVAIAK SILARFGNPE EVSEKEDGSE 130 140 150 160 170 180 EEAGTSGADE EGKQYKNTDQ LVGASLTCIF EVLEQLSRRD AELCVQALES LLSLIQSMPI 190 200 210 220 230 240 DCLQSENRLS MSAMMHVLKT LREDACPSVS SKATSCLVAL SVACGEPEHL GSTIRSLICM 250 260 270 280 290 300 KKNIRMSADS TYDMIQMPEN LRKLLLKVRR KALGGDNTAN SPPNWAMVDV HEHSVASSFS 310 320 330 340 350 360 LPSLPDSSPS SDTPDDDNRI HSTMACDGTF LYILNYVGLY KLGTGLNETI SGKLYAANQS 370 380 390 400 410 420 LQSSKNVQMY LCNGSLYLRR NYSSCISVID TDSLLDIGEV ILPPSCVQHA LFTDGTYFYS 430 440 450 460 470 480 ATLIANSTLS TIQLNDSFSP SNEPSSRRSH RLTDVKFTIQ GDLQVPHQLP EFLPANLHPQ 490 500 510 520 530 540 TVDLHFTREM AFIQARSGKV YYAGNGTRFG LFETGNNWME LCLPEPIVQI SVGIDTIMFR 550 560 570 580 590 600 SGAGHGWIAS VDDKKRNGRL RRLVPSNRRK IVHVCASGHV YGYVSENGKI FMGGLHTMRV 610 620 630 640 650 660 NVSSQMLNGL DNVMISSLAL GKSHGVAVTR NGHLFTWGLN NMNQCGRVES TSTTSSPRHS 670 680 690 700 710 720 GRQEYQICPI GEHTWLTDTP SVCAQCGLCS ARGVACGRVP RPKGTMCHCG VGESTCLRCG 730 740 750 760 770 780 LCRPCGEVTE PAQPGRAQHV QFSSTAAPQR STLHPSRVIL SQGPHDVKVS SVSCGNFHTV 790 800 810 820 830 840 LLASDRRVFT FGSNCHGQLG VGDTLSKNTP QQVILPSDTV IVQVAAGSNH TILRANDGSV 850 860 870 880 890 900 FTFGAFGKGQ LARPAGEKAG WNAIPEKVSG FGPGFNAFAG WIGADGDSSI IHSHTALLSS 910 920 930 940 950 960 DNILKAQIVA NKTNIFIFPR EVGKDYIVIR RKLNVFEHHA SDYKCWYTSW ATDPKYDMLW 970 980 990 1000 1010 1020 YYNSAEMEIK GYDIFKKSEK SVGDAFDSLT FLAGAEFAVQ VYDSPAYATS MSLGMQLLSA 1030 1040 1050 1060 1070 1080 TFSANVINLS EFWKEKHGER EQDHEKTIMD GYSVANRFDG TGGGWGYSAN SVEAIQFKVS 1090 1100 1110 1120 1130 1140 KEIRLVGVGL YGGRGEYISK LKLYRQIGTE ADELYVEQIT ETDETVYDCG AHETATLLFS 1150 1160 1170 1180 1190 1200 QPIVIQPNHW HVVSAKISGP SSDCGANGKR HVECDGVTFQ FRKSAVSNNG TDVDVGQIPE 1210 1220 1230 1240 1250 1260 LYYQIVGGSE SRDESDSNKQ LSISRDMSNL FSPAALKNVT AEGIGNLLIL LEWALQRVQI 1270 1280 1290 1300 1310 1320 DEDTNNQVEG SAENQWSQER AGFVAILSMK LISRFVRTVY KEKGCHDEPG IDFANKLVNL 1330 1340 1350 1360 1370 1380 HSMLLEFFFS TDMTGYENRP LIKKEEKVVE EGYTLMKCVS EAVKLFISLS HCFMGSRSLM 1390 1400 1410 1420 1430 1440 NAHLIAVMNK GNHEALILTS AIIGSLAKIE RFAHQLLCST TTTERFPMLS SLLLKHFNCE 1450 1460 1470 1480 1490 1500 KETLASLTSF PNILRFLYDQ TFMRNAYENT SSLAEAILVK VSRDLAIPTD DTLMGPVVHQ 1510 1520 1530 1540 1550 1560 TSSRFRRRSA QPTWDMSDGC ADAIAFRVDS EGIKLHGFGI YLPTEPDRRN FVGEIMMLSP 1570 1580 1590 1600 1610 1620 DSSEKWTCLL RVTAEMSSEE KEVGIVRFPE YVLLSPGVTY AVKVNMMKNT KTFCGEGGVT 1630 1640 1650 1660 1670 1680 QVHLLNGARL FFSGCSMSQN GTTVQRGQLP YLIYSILDQS NSLQIKQETI YDTFTLLLRL 1690 1700 1710 1720 1730 1740 MANKIGAAIT EGGALPACCQ HLMSHINPHV MVYMERFPDK ALEMMSTMEQ LIPMVSNLNG 1750 1760 1770 1780 1790 1800 VERVFHSYDS DDSGCDTPYS GIVTTVVESQ HPYKPNTSSS MVLLFEEADY ICVRFSPDCQ 1810 1820 1830 1840 1850 1860 TAQFDDQLTI YLKIDEHSYM PIERCYGSEW PSYPMILPGN CLMFVLDASS AVEGATSEQM 1870 1880 1890 1900 1910 1920 FGYHVTVTGY LVGYNDSTMR LEQDLVWLSA NACRIMTQLP INPSNIEHLS TAEDDTRHLF 1930 1940 1950 1960 1970 1980 EKHGSLLKKG LSLSHSPTLS ELCTKGQPPP AQSADLQFLR EFLSGHTSTS AGFLAKWLPT 1990 2000 2010 2020 2030 2040 GSVVDASKCQ LSLSHDDLIV GKAVTLKLLC KDQYDREVDC PKLQVEVFAS LGHRNPSSTI 2050 2060 2070 2080 2090 2100 HQNLHIGNLP SSLLIHQNPF QPIIVNHTRY MNIAAMPAYA NYSVEEIRLG FMIEELVKDR 2110 2120 2130 2140 2150 2160 VPLKSSDSSL FSGTWTPTTA GKYRIECKVD GSDISHTYTV EVTERPHRAG KGTITKPSGS 2170 2180 2190 2200 2210 2220 RRGAQMTVAR TVSIPFSSDF SGIRMRLGTT LASTSVGVIP RGALVEFIEE MDNDDGKWIR 2230 2240 2250 2260 2270 2280 LTDETALLYG CNQGVGQVWC LAYHRPLQRE LIPLKADTDR EKAVKLRRKE IEKESNGSKH 2290 2300 2310 2320 2330 2340 HSVSIDAKET YILSPNDVLQ VYSTPAPHSM IDGEKIIGPC DLMSSGWLAN RHGVWIKLTG 2350 2360 2370 2380 2390 2400 VEKYVLQKND PSSETSLSFS TNGNDEEDLE RPIERKKTRL PNALTPSVAD CIRAVFAAFV 2410 2420 2430 2440 2450 2460 WHEHLVKDLM AAAAYLRFHQ NLHNIWQSCE IPSCTNAPAA LQPIVKIWRE ICEVVETSVE 2470 2480 2490 2500 2510 2520 QHLIMPPVSN KAMRAETVKP PSRSGGCELC DANITVPLTV HLRMAHPGCG GDCLGYGYNS 2530 2540 2550 2560 2570 2580 NGKFTTGWSG ECGAGGRGQS PWYLLCNTCR SQYLKKTPAG HHQERTRRWR EFRFSTSASD 2590 2600 2610 2620 2630 2640 ARPEVIIRQN AMFLLDLNSR LQTESNSSST ATSGWTINLF PTHLSTPSTM PRSQQKRLDV 2650 2660 2670 2680 2690 2700 PPNNSVHQNS YMKLGYSSDP GPKVNVIMSP PNQGADQSAS LNRPGPSAIN EPAEVLQSPS 2710 2720 2730 2740 2750 2760 AALRTLFSNT NPSTSALLKR PVLAFCVEHH DLKRIKSACV QSVRRAVAFS HAFRVWNWLL 2770 2780 2790 2800 2810 2820 RMVSSEYSVS DIILQYLTTL TSYNRLAEYM FSAKKNSNIL PHPWRLCFLA GPIAADMVTQ 2830 2840 2850 2860 2870 2880 LHAFLHTVSI ILQSAGVDGR LKSLCFKSWT LQLTAQEQDL LILTCNILGT VGGILSDTSI 2890 2900 2910 2920 2930 2940 LDSDNRFVKE MKDITKFADI TASSRQAMVI CLTDESGETF WESGEEDKNR SRSLSVQLDE 2950 2960 2970 2980 2990 3000 SAHGEILSLF IDNARDEGYR ISSIAFKAIL EDGRRKDLTS LTLESAYCGW LKCCIKDISH 3010 3020 3030 3040 3050 3060 IQIQFKGPNP ASRIRQLMIL GYPAKTTGTP RLAPSTSHHL FFSDTQRDAF ALFQAISSQA 3070 3080 3090 3100 3110 3120 FCGELSEDDT LRERVIDLLF SRVQLYPLQN YVYTQVVQAM EKEVELLCDK SKRNYSYCCG 3130 3140 3150 3160 3170 3180 LMSLLVRICD SRGNMDSFGQ RNSVLTSITQ LLIFSPVVVQ RQCLNSLECI FASFTPSNVE 3190 3200 3210 3220 3230 3240 VPKIIRNLLV VVGKVIQLQV RDKAAHTVVT VHLCSSVLNA PQNWRVDKSI DMDIGRQTAV 3250 3260 3270 3280 3290 3300 LVENLCNGTY TPEWSNATKC ELANCLLSLI QMPESVSYTE TLSTGGKSKA VAVVSSKRFW 3310 3320 3330 3340 3350 3360 TAISSLSLIK DKSWLELSER WKTVQDEEDQ EPVLLCENHD DGHTVAQVFC VDCDVALCKE 3370 3380 3390 3400 3410 3420 CFTVMHLHKK NRNHGVKNLV QSSTQHDINI HQGCARMKFL NFLILFHGEA LNGMVEVAAD 3430 3440 3450 3460 3470 3480 TLFPTSTSSI QPAMQSSSAF LGIHPMTCRF CGNNVPVEDQ SLDGTCTHED CVNYAKTACQ 3490 3500 3510 3520 3530 3540 VMHTCNHFCG GIRNEEECLP CMTCKREDAA QDGDDVCVIC FTERLGAAPC IRLGCGHMFH 3550 3560 3570 3580 3590 3600 FHCVRMILER RWNGPRIVFR FMQCPLCIQP IEHSGLQDLI EPLKTIRQEV VDKAKMRLEY 3610 3620 3630 3640 3650 3660 DGLLTTPALT DPRSEFYNQP EEYALDRYMY VLCHKCKKAY FGGESRCQAA LDSSQFNPEE 3670 3680 3690 3700 3710 3720 LLCGGCSDTS GVQVCPRHGV EYLEYKCRFC CSIAVYFCFG TTHFCAPCHD DFQRLMSLPK 3730 3740 3750 3760 HLLPTCPVGP RSTPMEEQTC PLKMKHPPTG DEFAMGCGIC RNISTF

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Regulation of presynaptic terminal organization by C. elegans RPM-1, a putative guanine nucleotide exchanger with a RING-H2 finger domain." Zhen M., Huang X., Bamber B., Jin Y. Neuron 26:331-343(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, TISSUE SPECIFICITY, MUTAGENESIS OF ARG-3597 AND CYS-3675. Strain: Bristol N2.
[2]	"rpm-1, a conserved neuronal gene that regulates targeting and synaptogenesis in C. elegans." Schaefer A.M., Hadwiger G.D., Nonet M.L. Neuron 26:345-356(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE. Strain: Bristol N2.
[3]	"Genome sequence of the nematode C. elegans: a platform for investigating biology." The C. elegans sequencing consortium Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Bristol N2.
[4]	Bienvenut W.V. Submitted (MAR-2005) to UniProtKB Cited for: PROTEIN SEQUENCE OF 86-99; 341-351; 621-629; 736-749; 834-847; 858-865; 1045-1056; 1084-1093; 1225-1237; 1281-1290; 1426-1434; 1441-1480; 1588-1603; 1961-1988; 2089-2097; 2103-2122; 2171-2183; 2186-2201; 2408-2416 AND 2573-2588, MASS SPECTROMETRY.
[5]	"Regulation of a DLK-1 and p38 MAP kinase pathway by the ubiquitin ligase RPM-1 is required for presynaptic development." Nakata K., Abrams B., Grill B., Goncharov A., Huang X., Chisholm A.D., Jin Y. Cell 120:407-420(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	FO080217 Genomic DNA. Translation: CCD62087.1.
PIR	T29165.
RefSeq	NP_505267.1. NM_072866.3.
3D structure databases
ProteinModelPortal	Q17551.
SMR	Q17551. Positions 764-846, 1049-1205, 1503-1654, 3512-3590.
ModBase	Search...
Protein-protein interaction databases
STRING	6239.C01B7.6.
Proteomic databases
PaxDb	Q17551.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblMetazoa	C01B7.6; C01B7.6; C01B7.6.
GeneID	179259.
KEGG	cel:CELE_C01B7.6.
UCSC	C01B7.6. c. elegans.
Organism-specific databases
CTD	179259.
WormBase	C01B7.6; CE06730; WBGene00004457; rpm-1.
Phylogenomic databases
eggNOG	NOG240798.
GeneTree	ENSGT00390000011403.
HOGENOM	HOG000016145.
InParanoid	Q17551.
KO	K10693.
OMA	LLSILHW.
Enzyme and pathway databases
UniPathway	UPA00143.
Family and domain databases
Gene3D	2.130.10.30. 1 hit. 3.30.40.10. 1 hit.
InterPro	IPR004939. APC_su10/DOC_dom. IPR008979. Galactose-bd-like. IPR027047. Highwire/Pam/Rpm-1. IPR012983. PHR. IPR009091. RCC1/BLIP-II. IPR000408. Reg_chr_condens. IPR000315. Znf_B-box. IPR001841. Znf_RING. IPR013083. Znf_RING/FYVE/PHD. [Graphical view]
PANTHER	PTHR12846. PTHR12846. 1 hit.
Pfam	PF08005. PHR. 2 hits. PF00415. RCC1. 1 hit. PF00643. zf-B_box. 1 hit. PF13639. zf-RING_2. 1 hit. [Graphical view]
SMART	SM00336. BBOX. 1 hit. SM00184. RING. 1 hit. [Graphical view]
SUPFAM	SSF49785. Gal_bind_like. 1 hit. SSF50985. RCC1/BLIP-II. 1 hit.
PROSITE	PS51284. DOC. 1 hit. PS00625. RCC1_1. False negative. PS00626. RCC1_2. 1 hit. PS50012. RCC1_3. 1 hit. PS50119. ZF_BBOX. 1 hit. PS00518. ZF_RING_1. False negative. PS50089. ZF_RING_2. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	904596.

Entry information

Entry name

RPM1_CAEEL

Accession

Primary (citable) accession number: Q17551

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 21, 2005
Last sequence update:	November 1, 1996
Last modified:	May 1, 2013
This is version 107 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Caenorhabditis annotation project