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SEC65/YML105C Single Page Format

This page provides an alternative format to the SGD Locus Summary Page. Note that additional information may be available on or linked from the standard format SGD Locus Summary page.

Contents

Names and Identifiers GO Annotations Pathways Summary Paragraph Mutant Phenotypes Interactions Homologs Protein Info (physical properties, transcript info) PDB Homologs (protein structure info) Motifs Genome-wide Expression (and other large-scale analyses) Locus History (misc. notes) Sequence Retrieval and Analysis Map and Displays Localization Community Annotation Literature Guide

Sequence Coordinates   ChrXIII: 58687 to 57866 CDS: 58687 - 57866 Click on map for expanded view SGD ORF map GBrowse

SGD Locus Page

Names and Identifiers [TOP] [NEXT]
Standard Name	Systematic Name	Alias	Feature Type	SGDID
SEC65	YML105C		ORF, Verified	S000004573
Description
Subunit of the signal recognition particle (SRP), involved in protein targeting to the ER; interacts with Srp54p; homolog of mammalian SRP19

GO Annotations [TOP] [NEXT]
Molecular Function Annotation(s) Reference(s) Evidence Assigned By 7S RNA binding Van Nues RW and Brown JD (2004) Saccharomyces SRP RNA secondary structures: a conserved S-domain and extended Alu-domain. RNA 10(1):75-89        IDA : Inferred from Direct Assay Assigned on 2008-07-28 SGD DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR002778 Assigned on 2007-05-23 UniProtKB peptide binding Tian W, et al. (2008) Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biol 9 Suppl 1:S7              RCA : Reviewed Computational Analysis Assigned on 2009-09-03 YeastFunc signal sequence binding Tian W, et al. (2008) Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biol 9 Suppl 1:S7              RCA : Reviewed Computational Analysis Assigned on 2009-09-03 YeastFunc
Biological Process Annotation(s) Reference(s) Evidence Assigned By SRP-dependent cotranslational protein targeting to membrane DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR002778 Assigned on 2008-02-13 UniProtKB SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition Hann BC, et al. (1992) SEC65 gene product is a subunit of the yeast signal recognition particle required for its integrity. Nature 356(6369):532-3      IMP : Inferred from Mutant Phenotype Assigned on 2002-12-02 SGD protein complex assembly Huttenhower C and Troyanskaya OG (2009) Prediction of Gene Ontology annotations by integrating high-throughput datasets    RCA : Reviewed Computational Analysis Assigned on 2009-08-06 bioPIXIE_MEFIT protein targeting to ER Stirling CJ and Hewitt EW (1992) The S. cerevisiae SEC65 gene encodes a component of yeast signal recognition particle with homology to human SRP19. Nature 356(6369):534-7      IMP : Inferred from Mutant Phenotype Assigned on 2003-10-20 SGD
Cellular Component Annotation(s) Reference(s) Evidence Assigned By cytoplasm GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0963 Assigned on 2008-02-14 UniProtKB GOA curators and UniProt curators (2007) Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping.      IEA : Inferred from Electronic Annotation with EBI:SL-0086 Assigned on 2008-02-13 UniProtKB ribonucleoprotein complex GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0687 Assigned on 2007-05-23 UniProtKB signal recognition particle DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR002778 Assigned on 2008-02-13 UniProtKB signal recognition particle, endoplasmic reticulum targeting Hann BC, et al. (1992) SEC65 gene product is a subunit of the yeast signal recognition particle required for its integrity. Nature 356(6369):532-3      IDA : Inferred from Direct Assay Assigned on 2002-12-02 SGD Stirling CJ and Hewitt EW (1992) The S. cerevisiae SEC65 gene encodes a component of yeast signal recognition particle with homology to human SRP19. Nature 356(6369):534-7      ISS : Inferred from Sequence or structural Similarity IMP : Inferred from Mutant Phenotype Assigned on 2003-10-20 SGD GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0733 Assigned on 2008-02-14 UniProtKB

Pathways [TOP] [NEXT]
No pathways available

Summary Paragraph [TOP] [NEXT]

SUMMARY PARAGRAPH for SEC65/YML105C for SEC65 The signal recognition particle (SRP) is an abundant and conserved ribonucleoprotein necessary for targeting proteins to the endoplasmic reticulum membrane (1). SRP in eukaryotes contains six subunits and a 7S RNA molecule; in S. cerevisiae the subunits are encoded by SRP14, SRP21, SRP68, SRP72, SEC65, and SRP54, and the RNA (termed scR1) is encoded by SCR1 (1, 2). With the exception of Srp54p, the proteins and RNA assemble into a core complex in the nucleus; this particle is exported to the cytoplasm where Srp54p joins to form the complete complex (3). Sec65p is required for association of Srp54p with the SRP particle (4). Loss of any of the SRP components causes a slow growth phenotype and loss of SRP-mediated translocation, but not cell death, indicating that the signal recognition particle is not essential in yeast and SRP-independent translocation can occur (1, 2). The first step of SRP-mediated cotranslational targeting is interaction between SRP and the ribosome nascent chain complex (RNC), which is comprised of the translating ribosome and the emerging nascent protein. SRP interacts with the RNC through the N-terminal hydrophobic signal sequence of the nascent protein. SRP then directs the RNC to the ER membrane via interaction between SRP and a signal receptor complex (SR), encoded by SRP101 and SRP102. Finally, the RNC is transferred to the translocon, a protein-conducting membrane channel, and SRP and the SR dissociate. GTP binding by both SRP (via the Srp54p subunit) and the SR is critical for their interaction, and GTP hydrolysis facilitates their dissociation (reviewed in 5, and see 5 for more details). Last Updated: 2008-08-11

Basic References [TOP]

BASIC INFORMATION REFERENCES forSEC65/YML105C for SEC65 1) Hann BC and Walter P (1991) The signal recognition particle in S. cerevisiae. Cell 67(1):131-44        2) Brown JD, et al. (1994) Subunits of the Saccharomyces cerevisiae signal recognition particle required for its functional expression. EMBO J 13(18):4390-400      3) Ciufo LF and Brown JD (2000) Nuclear export of yeast signal recognition particle lacking Srp54p by the Xpo1p/Crm1p NES-dependent pathway. Curr Biol 10(20):1256-64        4) Stirling CJ and Hewitt EW (1992) The S. cerevisiae SEC65 gene encodes a component of yeast signal recognition particle with homology to human SRP19. Nature 356(6369):534-7      5) Wild K, et al. (2004) SRP meets the ribosome. Nat Struct Mol Biol 11(11):1049-53        6) Hann BC, et al. (1992) SEC65 gene product is a subunit of the yeast signal recognition particle required for its integrity. Nature 356(6369):532-3

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for SEC65/YML105C

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for SEC65/YML105C

Homologs [TOP] [NEXT]
Comparison Resources PSI-BLAST Results Ashbya Homologs (AGD) BLASTN vs. fungi BLASTP at NCBI BLASTP vs. fungi Candida Homologs (CGD) Candida Homologs (CandidaDB) Fungal Alignment Fungal Orthogroups Repository Ortholog Search (P-POD) PhylomeDB Synteny Viewer Yeast Gene Order Browser (YGOB) eukarYotic OrtholoGY (YOGY)

Physical Properties and Transcript Information: predicted from sequence [TOP] [NEXT]
Protein Sequence Calculations from Predicted Full length Translation N-term MPRLEEI C-term KYKVVRR Length(aa) 273 MW(Da) 31,170 pI 9.8 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias 0.158   Codon Adaptation Index 0.173   Frequency of Optimal Codons 0.502   Hydropathicity of Protein -0.740   Aromaticity Score 0.073	10 20 30 40 50 | | | | | MPRLEEIDDFNDIDDLDMELAELDPSLRTPIAPKITPKVVRSQDQENPAF LPGTNNNSNSNNNSSNEKEQLSFINPKTGKVERSEAISKKDLEEVKRFQV LYPCYFDINRSHKEGRRVPKELAVENPLAKTMADAVRELGILCIFEGEKC HPQDFGNPGRIRVLFKENGQLIGAATKFKGGKRQLMKAVGEYMKRHPTTI ESLREIPYGPDFDNIEFKKIPRVKGFKMNEIVPLHSPFLMGHPMTKSVYE TPKITAAEKSFKPPKNKYKVVRR*

Protein Structures from PDB: proteins of known structure with sequence similarity to SEC65/YML105C, based on Smith-Waterman analysis. [TOP] [NEXT]

PDB protein structure(s) homologous to SEC65 Homolog Source (per PDB) Protein Alignment: SEC65 vs. Homolog External Links P-Value %Identical %Similar Alignment 1l9a ( Chain: A) Crystal structure of srp19 in complex with the s domain of signal recognition particle rna PDB_Info PDB_Structure Methanocaldococcus jannaschii 2.6e-05 35 32 View alignment SCOP MMDB CATH 2v3c ( Chain: A, B) Crystal structure of the srp54-srp19-7s.s srp rna complex of m. jannaschii PDB_Info PDB_Structure Methanocaldococcus jannaschii Chain A = 7.3e-05 35 31 View alignment SCOP MMDB CATH Chain B = 7.3e-05 35 31 View alignment 1lng ( Chain: A) Crystal structure of the srp19-7s.s srp rna complex of m. jannaschii PDB_Info PDB_Structure Methanocaldococcus jannaschii 7.3e-05 35 31 View alignment SCOP MMDB CATH 1mfq ( Chain: B) Crystal structure analysis of a ternary s-domain complex of human signal recognition particle PDB_Info PDB_Structure Homo sapiens 0.000139 35 29 View alignment SCOP MMDB CATH 2go5 ( Chain: B) Structure of signal recognition particle receptor (sr) in complex with signal recognition particle (srp) and ribosome nascent chain complex PDB_Info PDB_Structure Canis sp. | Triticum sp. | Homo sapiens | Mus musculus 0.000139 35 29 View alignment SCOP MMDB CATH 2j37 ( Chain: B) Model of mammalian srp bound to 80s rncs PDB_Info PDB_Structure Homo sapiens | Canis sp. | Triticum sp. | Triticum sp | Haloarcula marismortui 0.000139 35 29 View alignment SCOP MMDB CATH 1ry1 ( Chain: B) Structure of the signal recognition particle interacting with the elongation-arrested ribosome PDB_Info PDB_Structure Homo sapiens | Thermus aquaticus | Mus musculus | Tursiops truncatus 0.000139 35 29 View alignment SCOP MMDB CATH 1jid ( Chain: A) Human srp19 in complex with helix 6 of human srp rna PDB_Info PDB_Structure Homo sapiens 0.000169 35 29 View alignment SCOP MMDB CATH

Genome-wide Expression and Other Large-Scale Analyses [TOP] [NEXT]
Functional Analysis Expression Connection Summary Cell cycle and metabolic oscillation Cell cycle transcript profile Cyclebase Genevestigator GermOnline SPELL Microarray Search YGAC Triples Yeast Microarray Global Viewer YeastFunc	You can also search multiple datasets simultaneously using Expression Connection for expression studies or Function Junction for other large scale analyses.

Locus History (misc. notes) [TOP] [NEXT]

Nomenclature History

Standard Name	Reference
SEC65	Hann BC, et al. (1992) SEC65 gene product is a subunit of the yeast signal recognition particle required for its integrity. Nature 356(6369):532-3

Sequence Retrieval [TOP] [NEXT]
Sequence Type	Output Format
Genomic DNA	GCG | FASTA | NoHeader
Genomic DNA with 1 kb up and downstream	GCG | FASTA | NoHeader
DNA coding sequence (without introns, without flanking regions)	GCG | FASTA | NoHeader
Protein Translation of ORF	GCG | FASTA | NoHeader
6-Frame Translation(with Restriction Map)	GCG
Restriction Fragment Sizes	GCG
Sequence Analysis Tools BLASTP BLASTN Design Primers FASTA aa FASTA nt Restriction Fragment Map Restriction Fragment Sizes Six-Frame Translation

Sequence from other databases
Sequence ID	Source
YML105C	SGD Systematic Sequence
854866	NCBI: Gene ID
NP_013602.1	NCBI: RefSeq protein version ID
NP_013602.1	NCBI: RefSeq protein version ID
6323531	NCBI: NCBI protein GI

Map and Displays [TOP] [NEXT]
Physical, Genetic Maps:	Chromosomal Feature Map	GBrowse	Combined Physical and Genetic Map	Genetic Distance vs. Physical Distance Ratios
Similarity Viewers:	Synteny Viewer	Genomic Stripe View	SAGE Results Map

Localization [TOP] [NEXT]
Localization Resources YeastRC Localization (Seattle) YGAC Triples YeastGFP DB (UCSF) at SGD

Community Annotation [TOP] [NEXT]
No community annotation available.

Literature Guide: papers categorized by topic. [TOP]
Topics	Reference	Other Genes Addressed
29 curated references; 0 references not yet curated
Reviews	Fonzi WA (2009) The protein secretory pathway of Candida albicans. Mycoses	|BTT1 |EGD1 |EGD2 |GEA1 |GEA2 |GSG1 |NCE101 |NCE102 |SCR1 |SEC14 |SEC3 |SEC4 |SEC61 |SFB2 |MORE
Mutants/Phenotypes Strains/Constructs	Perry RJ, et al. (2009) Endoplasmic Reticulum-Associated Secretory Proteins Sec20p, Sec39p, and Dsl1p Are Involved in Peroxisome Biogenesis. Eukaryot Cell 8(6):830-843	|BOS1 |COP1 |DSL1 |PEX3 |POT1 |SEC1 |SEC11 |SEC12 |SEC13 |SEC14 |SEC17 |SEC18 |SEC20 |SEC21 |MORE
Mutants/Phenotypes Strains/Constructs	Angeles Juanes M, et al. (2008) Membrane topology and post-translational modification of the Saccharomyces cerevisiae essential protein Rot1. Yeast 25(2):93-106	|ROT1 |SEC61 |SEC62
Mutants/Phenotypes Strains/Constructs	Michelsen K, et al. (2007) Novel cargo-binding site in the beta and delta subunits of coatomer. J Cell Biol 179(2):209-17	|COP1 |DSL1 |ERG26 |PAC10 |PMP2 |RET2 |RET3 |RSC6 |SEC15 |SEC21 |SEC26 |SEC27 |SEC39 |SER33 |MORE
Regulation of Transcription	Kovalskaya ON, et al. (2006) Does a deficiency of the signal recognition particle (SRP)-pathway affect the biosynthesis of its components in Saccharomyces cerevisiae and Escherichia coli? Biochemistry (Mosc) 71(7):723-9	|SCR1 |SRP101 |SRP14 |SRP21 |SRP72
Genetic Interactions Mutants/Phenotypes Strains/Constructs	Pesheva MG, et al. (2006) Enhanced Protein Export in Saccharomyces cerevisiae nud1 Mutants Is an Active Process. Curr Microbiol 53(6):496-501	|COX10 |GAS1 |NUD1 |SEC1 |SEC7
Function/Process Mutants/Phenotypes Strains/Constructs	Altmann K and Westermann B (2005) Role of essential genes in mitochondrial morphogenesis in Saccharomyces cerevisiae. Mol Biol Cell 16(11):5410-7	|ARC35 |ARC40 |ARP2 |BFR2 |CCT4 |CCT6 |CDC34 |CDC53 |COF1 |DSL1 |ERG1 |ERG10 |ERG12 |ERG13 |MORE
Reviews	Pool MR (2005) Signal recognition particles in chloroplasts, bacteria, yeast and mammals (review). Mol Membr Biol 22(1-2):3-15	|SCR1 |SRP101 |SRP14 |SRP21 |SRP54 |SRP68 |SRP72
Fungal Related Genes/Proteins	Sims AH, et al. (2005) Transcriptome analysis of recombinant protein secretion by Aspergillus nidulans and the unfolded-protein response in vivo. Appl Environ Microbiol 71(5):2737-47	|BCH2 |EPT1 |INO1 |KAR2 |NCE102 |RPT3 |SEC27 |SEC63 |SEC72 |SHR3 |SLC1 |SRP54 |UBA1
Function/Process Protein-Nucleic Acid Interactions	Van Nues RW and Brown JD (2004) Saccharomyces SRP RNA secondary structures: a conserved S-domain and extended Alu-domain. RNA 10(1):75-89	|SCR1 |SRP54
Function/Process Mutants/Phenotypes Strains/Constructs	Willer M, et al. (2003) An in vitro assay using overexpressed yeast SRP demonstrates that cotranslational translocation is dependent upon the J-domain of Sec63p. Biochemistry 42(23):7171-7	|SCR1 |SEC63 |SRP14 |SRP21 |SRP54 |SRP68 |SRP72
Cellular Location	Grosshans H, et al. (2001) Biogenesis of the signal recognition particle (SRP) involves import of SRP proteins into the nucleolus, assembly with the SRP-RNA, and Xpo1p-mediated export. J Cell Biol 153(4):745-62	|CRM1 |DIS3 |KAP123 |MEX67 |MTR10 |NSP1 |NUP159 |NUP85 |PSE1 |RNA1 |RRP4 |SCR1 |SRM1 |SRP1 |MORE
DNA/RNA Sequence Features Fungal Related Genes/Proteins	Sanchez M and Dominguez A (2001) Gene order in a 10 275 bp fragment of Yarrowia lipolytica, including adjacent YlURA5 and YlSEC65 genes conserved in four yeast species. Yeast 18(9):807-13	|CYM1 |RPF1 |URA5
Function/Process Genetic Interactions Mutants/Phenotypes Strains/Constructs	Young BP, et al. (2001) Sec63p and Kar2p are required for the translocation of SRP-dependent precursors into the yeast endoplasmic reticulum in vivo. EMBO J 20(1-2):262-71	|KAR2 |SEC62 |SEC63 |SEC66 |SEC72
Cellular Location Function/Process Protein Processing/Modification/Regulation Techniques and Reagents	Ciufo LF and Brown JD (2000) Nuclear export of yeast signal recognition particle lacking Srp54p by the Xpo1p/Crm1p NES-dependent pathway. Curr Biol 10(20):1256-64	|CRM1 |SCR1 |SRP14 |SRP21 |SRP54 |SRP68 |SRP72 |YRB2
Function/Process Mutants/Phenotypes Non-Fungal Related Genes/Proteins Strains/Constructs	Prinz WA, et al. (2000) Mutants affecting the structure of the cortical endoplasmic reticulum in Saccharomyces cerevisiae. J Cell Biol 150(3):461-74	|ACT1 |CDC48 |SEC23 |SEC27 |TUB1 |TUB2 |TUB3 |UFE1
Fungal Related Genes/Proteins	Bai X, et al. (1999) The URA5 gene encoding orotate-phosphoribosyl transferase of the yeast Kluyveromyces lactis: cloning, sequencing and use as a selectable marker. Yeast 15(13):1393-8	|URA5
Function/Process Mutants/Phenotypes Strains/Constructs	Paunola E, et al. (1998) Folding of active beta-lactamase in the yeast cytoplasm before translocation into the endoplasmic reticulum. Mol Biol Cell 9(4):817-27	|HSP150 |SSA1 |SSA2 |SSA3 |SSA4
Function/Process Fungal Related Genes/Proteins Mutants/Phenotypes Non-Fungal Related Genes/Proteins Protein Physical Properties Protein Sequence Features Protein/Nucleic Acid Structure Strains/Constructs	Regnacq M, et al. (1998) Deletion analysis of yeast Sec65p reveals a central domain that is sufficient for function in vivo. Mol Microbiol 29(3):753-62
Non-Fungal Related Genes/Proteins	Chittenden K, et al. (1997) Interaction of rice and human SRP19 polypeptides with signal recognition particle RNA. Plant Mol Biol 34(3):507-15
Function/Process Fungal Related Genes/Proteins Mutants/Phenotypes Strains/Constructs	Sanchez M, et al. (1997) Isolation and cloning of the Yarrowia lipolytica SEC65 gene, a component of the yeast signal recognition particle displaying homology with the human SRP19 gene. Gene 203(1):75-84
Function/Process Genetic Interactions Mutants/Phenotypes	Ogg SC and Walter P (1995) SRP samples nascent chains for the presence of signal sequences by interacting with ribosomes at a discrete step during translation elongation. Cell 81(7):1075-84
Function/Process Mutants/Phenotypes Protein-Nucleic Acid Interactions Protein-protein Interactions Techniques and Reagents	Brown JD, et al. (1994) Subunits of the Saccharomyces cerevisiae signal recognition particle required for its functional expression. EMBO J 13(18):4390-400	|SCR1 |SRP14 |SRP21 |SRP54 |SRP68 |SRP72
Function/Process Mutants/Phenotypes Techniques and Reagents	Chang A, et al. (1993) Folding and intracellular transport of the yeast plasma-membrane H(+)-ATPase: effects of mutations in KAR2 and SEC65. Proc Natl Acad Sci U S A 90(12):5808-12	|KAR2
Function/Process Fungal Related Genes/Proteins Mutants/Phenotypes Strains/Constructs Techniques and Reagents	Kean LS, et al. (1993) Retrograde lipid traffic in yeast: identification of two distinct pathways for internalization of fluorescent-labeled phosphatidylcholine from the plasma membrane. J Cell Biol 123(6 Pt 1):1403-19	|CHC1 |SEC1 |SEC11 |SEC12 |SEC14 |SEC17 |SEC18 |SEC2 |SEC21 |SEC4 |SEC6 |SEC63 |SEC7
DNA/RNA Sequence Features Function/Process Genetic Interactions Mutants/Phenotypes Non-Fungal Related Genes/Proteins Protein Sequence Features Regulatory Role Strains/Constructs	Hann BC, et al. (1992) SEC65 gene product is a subunit of the yeast signal recognition particle required for its integrity. Nature 356(6369):532-3	|SRP54
DNA/RNA Sequence Features Genetic Interactions Non-Fungal Related Genes/Proteins Protein Sequence Features Strains/Constructs	Stirling CJ and Hewitt EW (1992) The S. cerevisiae SEC65 gene encodes a component of yeast signal recognition particle with homology to human SRP19. Nature 356(6369):534-7	|SRP54
Fungal Related Genes/Proteins Mutants/Phenotypes	Stirling CJ, et al. (1992) Protein translocation mutants defective in the insertion of integral membrane proteins into the endoplasmic reticulum. Mol Biol Cell 3(2):129-42	|HMG1 |SEC61 |SEC62 |SEC63
Non-Fungal Related Genes/Proteins	Zopf D, et al. (1990) The methionine-rich domain of the 54 kd protein subunit of the signal recognition particle contains an RNA binding site and can be crosslinked to a signal sequence. EMBO J 9(13):4511-7	|SCR1 |SRP54

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