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SPC2/YML055W 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: 164790 to 165326 CDS: 164790 - 165326 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
SPC2	YML055W	SPY1	ORF, Verified	S000004519
Description
Subunit of signal peptidase complex (Spc1p, Spc2p, Spc3p, Sec11p), which catalyzes cleavage of N-terminal signal sequences of proteins targeted to the secretory pathway; homologous to mammalian SPC25

GO Annotations [TOP] [NEXT]
Molecular Function Annotation(s) Reference(s) Evidence Assigned By peptidase activity DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR009582 Assigned on 2008-10-13 UniProtKB protein binding Antonin W, et al. (2000) Interactions between Spc2p and other components of the endoplasmic reticulum translocation sites of the yeast Saccharomyces cerevisiae. J Biol Chem 275(44):34068-72        IMP : Inferred from Mutant Phenotype Assigned on 2001-01-18 SGD
Biological Process Annotation(s) Reference(s) Evidence Assigned By peptide metabolic process 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 maturation 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 processing 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 Mullins C, et al. (1996) Structurally related Spc1p and Spc2p of yeast signal peptidase complex are functionally distinct. J Biol Chem 271(46):29094-9        IGI : Inferred from Genetic Interaction with SGD:SEC11 IPI : Inferred from Physical Interaction with SGD:SEC11 IMP : Inferred from Mutant Phenotype Assigned on 2006-08-07 SGD signal peptide processing Mullins C, et al. (1996) Structurally related Spc1p and Spc2p of yeast signal peptidase complex are functionally distinct. J Biol Chem 271(46):29094-9        IPI : Inferred from Physical Interaction IGI : Inferred from Genetic Interaction ISS : Inferred from Sequence or structural Similarity Assigned on 2001-01-18 SGD Antonin W, et al. (2000) Interactions between Spc2p and other components of the endoplasmic reticulum translocation sites of the yeast Saccharomyces cerevisiae. J Biol Chem 275(44):34068-72        IPI : Inferred from Physical Interaction IMP : Inferred from Mutant Phenotype Assigned on 2001-01-18 SGD DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR009582 Assigned on 2007-05-23 UniProtKB
Cellular Component Annotation(s) Reference(s) Evidence Assigned By endoplasmic reticulum GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0256 Assigned on 2007-05-23 UniProtKB integral to membrane DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR009582 Assigned on 2007-05-23 UniProtKB GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0812 Assigned on 2007-05-23 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-9909 Assigned on 2009-10-01 UniProtKB membrane GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0472 Assigned on 2007-05-23 UniProtKB signal peptidase complex YaDeau JT, et al. (1991) Yeast signal peptidase contains a glycoprotein and the Sec11 gene product. Proc Natl Acad Sci U S A 88(2):517-21        IDA : Inferred from Direct Assay Assigned on 2001-01-18 SGD DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR009582 Assigned on 2007-05-23 UniProtKB

Pathways [TOP] [NEXT]
No pathways available

Summary Paragraph [TOP] [NEXT]

SUMMARY PARAGRAPH for SPC2/YML055W for SPC2 SPC2 encodes a subunit of the signal peptidase complex (SPC), which cleaves the signal sequence from proteins targeted to the endoplasmic reticulum (ER) (1). Signal peptide cleavage occurs concomitantly with translocation through the translocon pore into the ER. In yeast, translocation can occur cotranslationally or posttranslationally, whereas in mammals translocation is always cotranslational. The process of protein translocation into the ER is reviewed in references 2 and 3. The yeast SPC comprises four proteins, Spc1p, Spc2p, Spc3p, and Sec11p (4, 5). Spc2p is homologous to the mammalian signal peptidase subunit SPC25 (1). Spc2p is not essential for viability or for signal peptidase activity (1, 5), but deletion of SPC2 reduces signal peptidase activity in vitro (5). The spc2 null mutant also shows reduced levels of the other SPC subunits (5), and is synthetically lethal with a temperature-sensitive mutation in SEC11 (1). Spc2p can be coimmunoprecipitated with Sbh1p and Sbh2p, which are beta subunits of two different "Sec61" complexes involved in ER membrane translocation (5, 3). The genetic and physical interactions observed suggest that Spc2p may facilitate interactions between different components of the translocation machinery (5). Last Updated: 2000-11-28

Basic References [TOP]

BASIC INFORMATION REFERENCES forSPC2/YML055W for SPC2 1) Mullins C, et al. (1996) Structurally related Spc1p and Spc2p of yeast signal peptidase complex are functionally distinct. J Biol Chem 271(46):29094-9        2) Rapoport TA, et al. (1996) Protein transport across the eukaryotic endoplasmic reticulum and bacterial inner membranes. Annu Rev Biochem 65:271-303      3) Johnson AE and van Waes MA (1999) The translocon: a dynamic gateway at the ER membrane. Annu Rev Cell Dev Biol 15:799-842        4) YaDeau JT, et al. (1991) Yeast signal peptidase contains a glycoprotein and the Sec11 gene product. Proc Natl Acad Sci U S A 88(2):517-21        5) Antonin W, et al. (2000) Interactions between Spc2p and other components of the endoplasmic reticulum translocation sites of the yeast Saccharomyces cerevisiae. J Biol Chem 275(44):34068-72        6) Fang H, et al. (1997) In addition to SEC11, a newly identified gene, SPC3, is essential for signal peptidase activity in the yeast endoplasmic reticulum. J Biol Chem 272(20):13152-8        7) Meyer HA and Hartmann E (1997) The yeast SPC22/23 homolog Spc3p is essential for signal peptidase activity. J Biol Chem 272(20):13159-64

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for SPC2/YML055W

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for SPC2/YML055W

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 MSSAKPI C-term LDTKKNE Length(aa) 178 MW(Da) 20,802 pI 10.07 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias 0.098   Codon Adaptation Index 0.145   Frequency of Optimal Codons 0.469   Hydropathicity of Protein -0.342   Aromaticity Score 0.152	10 20 30 40 50 | | | | | MSSAKPINVYSIPELNQALDEALPSVFARLNYERSYALLDAKLYIGYSIA VVAGLSFFLDKKFERDQIVTYQKLLVGAYFVLSLLFWYFSRFIEKGTVYV GKRRGTKEEIYVKTKFEKNEPLYLVELVQKKKGENSKKELKAKLEVNKVF NESGYLQNDAYFKWFSEQHNVLDTKKNE*

Protein Structures from PDB: proteins of known structure with sequence similarity to SPC2/YML055W, based on Smith-Waterman analysis. [TOP] [NEXT]
No protein structure information available.

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
SPC2	SGD (2007) Information without a citation in SGD

Mapping Notes

Date	Note
1996-09-21	Edition 13: Spc2p is the homologue to SPC25 of the mammalian signal peptidase complex. Cherry JM, et al. (1996) "Genetic and Physical Maps of Saccharomyces cerevisiae (Edition 13)". Pp. 361-364 in 1996 Yeast Genetics and Molecular Biology Meeting Program and Abstracts. Bethesda, MD: The Genetics Society of America

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
YML055W	SGD Systematic Sequence
854949	NCBI: Gene ID
NP_013657.1	NCBI: RefSeq protein version ID
NP_013657.1	NCBI: RefSeq protein version ID
6323586	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) Organelle DB (UMich) 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
8 curated references; 0 references not yet curated
Cell Cycle Phase Involved Mutants/Phenotypes Regulation of Strains/Constructs	Niu W, et al. (2008) Mechanisms of Cell Cycle Control Revealed by a Systematic and Quantitative Overexpression Screen in S. cerevisiae. PLoS Genet 4(7):e1000120	|ACT1 |AIM20 |ALG6 |AME1 |ARC1 |ARF1 |ASK1 |ATG26 |AVO2 |BET4 |BUL1 |CBF1 |CDC31 |CDC39 |MORE
Protein Physical Properties	White MA, et al. (2007) Characteristics affecting expression and solubilization of yeast membrane proteins. J Mol Biol 365(3):621-36	|ALG1 |ALG7 |APQ12 |AQY1 |ARE2 |ATG9 |ATP4 |BET1 |BIG1 |BOS1 |BRR6 |CAX4 |CHO1 |COS7 |MORE
Mutants/Phenotypes	Chen Y, et al. (2005) Identification of mitogen-activated protein kinase signaling pathways that confer resistance to endoplasmic reticulum stress in Saccharomyces cerevisiae. Mol Cancer Res 3(12):669-77	|ALG3 |ALG8 |ALG9 |ARD1 |BCK1 |CMR2 |CNB1 |DAL81 |DID2 |EDE1 |ERV25 |FPS1 |FYV8 |HAC1 |MORE
Cellular Location Function/Process Protein-protein Interactions Regulation of Techniques and Reagents	Antonin W, et al. (2000) Interactions between Spc2p and other components of the endoplasmic reticulum translocation sites of the yeast Saccharomyces cerevisiae. J Biol Chem 275(44):34068-72	|SBH1 |SBH2 |SEC11 |SEC61 |SPC1 |SPC3 |SSH1 |SSS1
Function/Process Fungal Related Genes/Proteins	Fang H, et al. (1997) In addition to SEC11, a newly identified gene, SPC3, is essential for signal peptidase activity in the yeast endoplasmic reticulum. J Biol Chem 272(20):13152-8	|SEC11 |SPC3
Function/Process Fungal Related Genes/Proteins	Meyer HA and Hartmann E (1997) The yeast SPC22/23 homolog Spc3p is essential for signal peptidase activity. J Biol Chem 272(20):13159-64	|SEC11 |SPC3
Function/Process Genetic Interactions Mutants/Phenotypes Non-Fungal Related Genes/Proteins Strains/Constructs	Mullins C, et al. (1996) Structurally related Spc1p and Spc2p of yeast signal peptidase complex are functionally distinct. J Biol Chem 271(46):29094-9	|SEC11 |SPC1
Cellular Location Other Features	YaDeau JT and Blobel G (1989) Solubilization and characterization of yeast signal peptidase. J Biol Chem 264(5):2928-34	|SEC11 |SPC1 |SPC3

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