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SED4/YCR067C 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   ChrIII: 236318 to 233121 CDS: 236318 - 233121 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
SED4	YCR067C		ORF, Verified	S000000663
Description
Integral endoplasmic reticulum membrane protein, functions as a positive regulator of Sar1p probably through inhibition of GTPase activation by Sec23p; binds Sec16p, participates in vesicle formation, similar to Sec12p

GO Annotations [TOP] [NEXT]
Molecular Function Annotation(s) Reference(s) Evidence Assigned By GTPase activator activity GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0343 Assigned on 2008-02-14 UniProtKB molecular_function unknown SGD (2002) Use of the ND evidence code for Gene Ontology (GO) terms in SGD    ND : No Biological Data Available Assigned on 2010-01-05 SGD
Biological Process Annotation(s) Reference(s) Evidence Assigned By COPII-coated vesicle budding Gimeno RE, et al. (1995) SED4 encodes a yeast endoplasmic reticulum protein that binds Sec16p and participates in vesicle formation. J Cell Biol 131(2):325-38      IGI : Inferred from Genetic Interaction with SGD:SEC23, SGD:SEC13 Assigned on 2010-01-05 SGD negative regulation of GTPase activity Saito-Nakano Y and Nakano A (2000) Sed4p functions as a positive regulator of Sar1p probably through inhibition of the GTPase activation by Sec23p. Genes Cells 5(12):1039-48        IDA : Inferred from Direct Assay Assigned on 2010-01-05 SGD protein transport GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0653 Assigned on 2007-05-23 UniProtKB transport GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0813 Assigned on 2007-05-23 UniProtKB vesicle-mediated transport GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0931 Assigned on 2008-02-14 UniProtKB
Cellular Component Annotation(s) Reference(s) Evidence Assigned By Golgi apparatus GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0333 Assigned on 2008-02-14 UniProtKB 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 2009-10-01 UniProtKB integral to endoplasmic reticulum membrane Gimeno RE, et al. (1995) SED4 encodes a yeast endoplasmic reticulum protein that binds Sec16p and participates in vesicle formation. J Cell Biol 131(2):325-38      IDA : Inferred from Direct Assay Assigned on 2005-04-19 SGD integral to membrane 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-9906 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

Pathways [TOP] [NEXT]
No pathways available

Summary Paragraph [TOP] [NEXT]

SUMMARY PARAGRAPH for SED4/YCR067C for SED4 Transport of proteins from the endoplasmic reticulum (ER) to the Golgi is mediated by COPII vesicles (1). The COPII vesicle coat is minimally comprised of 5 subunits: the GTPase Sar1p, the Sec23p-Sec24p heterodimer, and the Sec13p-Sec31p complex (2, 3, 4, 5). COPII vesicle coats can also contain heterodimers of Sec23p complexed with either of the Sec24p homologs, Sfb2p or Sfb3p (6, 7, 8). In S. cerevisiae, COPII vesicle formation occurs throughout the ER (9). In most other eukaryotes, COPII vesicle-mediated protein export is localized to specialized regions termed transitional ER (tER) or ER exit sites (ERES) (3). COPII vesicle formation requires the assembly of the COPII vesicle coat and cargo selection and is regulated by cycles of GTP hydrolysis. The GTP exchange factor (GEF) Sec12p, an ER membrane protein, activates Sar1p by exchanging GDP for GTP. Sar1p-GTP recruits the Sec23p-Sec24p heterodimer. Sec23p is a GTPase activating protein (GAP) for the Sar1p GTPase activity (10, 11, and reviewed in 3). Sec24p, Sfb2p, and Sfb3p, are involved in cargo selection (12, 8, 7). Sar1p, the Sec23p-Sec24p heterodimer, and cargo form the prebudding complex. Improper cargo selection results in GTP hydrolysis and diassembly of the prebudding complex (13). However, once the pre-budding complex is assembled, Sec13p and Sec31p polymerize to form the outer layer or scaffold of the COPII vesicle coat. The Sec13p-Sec31p complex further stimulates the GTPase activity of Sar1p (reviewed in 3). Although Sar1p, Sec23p, Sec24p, Sec13p, and Sec31p are necessary and sufficient for vesicle formation, additional factors such as Sec16p and Sed4p are also involved in this process. Through interactions with other COPII proteins, Sec16p is thought to facilitate the assembly of the vesicle coat by stabilizing the pre-budding complex (14) while Sed4p may regulate the vesicle budding process by inhibiting the GAP activity of Sec23p (15). Mutations in genes involved in COPII vesicle formation are also impaired in other processes such as ERAD (ER-associated degradation) and autophagy, suggesting that ER to the Golgi transport is a prerequisite for these processes to occur (16, 17, 18, 19). Mutations in the human homolog of SEC23, Sec23A, cause the autosomal recessive disorder Cranio-lenticulo sutural dysplasia (CLSD), while mutation of Sar1B, one of the two human isoforms of S. cerevisiae Sar1p, cause defects in lipoprotein metabolism including the diseases that are known as the chylomicron retention diseases (CMRDs) (reviewed in 3). Last Updated: 2010-01-07

Basic References [TOP]

BASIC INFORMATION REFERENCES forSED4/YCR067C for SED4 1) Bonifacino JS and Glick BS (2004) The mechanisms of vesicle budding and fusion. Cell 116(2):153-66        2) Lee MC and Miller EA (2007) Molecular mechanisms of COPII vesicle formation. Semin Cell Dev Biol 18(4):424-34        3) Hughes H and Stephens DJ (2008) Assembly, organization, and function of the COPII coat. Histochem Cell Biol 129(2):129-51        4) Barlowe C, et al. (1994) COPII: a membrane coat formed by Sec proteins that drive vesicle budding from the endoplasmic reticulum. Cell 77(6):895-907        5) Fath S, et al. (2007) Structure and organization of coat proteins in the COPII cage. Cell 129(7):1325-36          6) Peng R, et al. (2000) Evidence for overlapping and distinct functions in protein transport of coat protein Sec24p family members. J Biol Chem 275(15):11521-8        7) Miller E, et al. (2002) Cargo selection into COPII vesicles is driven by the Sec24p subunit. EMBO J 21(22):6105-13          8) Miller EA, et al. (2003) Multiple cargo binding sites on the COPII subunit Sec24p ensure capture of diverse membrane proteins into transport vesicles. Cell 114(4):497-509      9) Rossanese OW, et al. (1999) Golgi structure correlates with transitional endoplasmic reticulum organization in Pichia pastoris and Saccharomyces cerevisiae. J Cell Biol 145(1):69-81        10) Barlowe C, et al. (1993) Purification and characterization of SAR1p, a small GTP-binding protein required for transport vesicle formation from the endoplasmic reticulum. J Biol Chem 268(2):873-9      11) Yoshihisa T, et al. (1993) Requirement for a GTPase-activating protein in vesicle budding from the endoplasmic reticulum. Science 259(5100):1466-8      12) Shimoni Y, et al. (2000) Lst1p and Sec24p cooperate in sorting of the plasma membrane ATPase into COPII vesicles in Saccharomyces cerevisiae. J Cell Biol 151(5):973-84        13) Sato K and Nakano A (2005) Dissection of COPII subunit-cargo assembly and disassembly kinetics during Sar1p-GTP hydrolysis. Nat Struct Mol Biol 12(2):167-74        14) Supek F, et al. (2002) Sec16p potentiates the action of COPII proteins to bud transport vesicles. J Cell Biol 158(6):1029-38        15) Saito-Nakano Y and Nakano A (2000) Sed4p functions as a positive regulator of Sar1p probably through inhibition of the GTPase activation by Sec23p. Genes Cells 5(12):1039-48        16) Taxis C, et al. (2002) ER-golgi traffic is a prerequisite for efficient ER degradation. Mol Biol Cell 13(6):1806-18        17) Hamasaki M, et al. (2003) The early secretory pathway contributes to autophagy in yeast. Cell Struct Funct 28(1):49-54        18) Fu L and Sztul E (2003) Traffic-independent function of the Sar1p/COPII machinery in proteasomal sorting of the cystic fibrosis transmembrane conductance regulator. J Cell Biol 160(2):157-63        19) Ishihara N, et al. (2001) Autophagosome requires specific early Sec proteins for its formation and NSF/SNARE for vacuolar fusion. Mol Biol Cell 12(11):3690-702        20) Hardwick KG, et al. (1992) Genes that allow yeast cells to grow in the absence of the HDEL receptor. EMBO J 11(11):4187-95      21) Gimeno RE, et al. (1995) SED4 encodes a yeast endoplasmic reticulum protein that binds Sec16p and participates in vesicle formation. J Cell Biol 131(2):325-38

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for SED4/YCR067C

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for SED4/YCR067C

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 MSGNSAN C-term AGLHDEL Length(aa) 1,065 MW(Da) 114,078 pI 4.45 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias 0.085   Codon Adaptation Index 0.134   Frequency of Optimal Codons 0.462   Hydropathicity of Protein -0.176   Aromaticity Score 0.061

10 20 30 40 50 | | | | | MSGNSANYDVGYPIYGAKFINEGTLLVAGGGGQFNSSFPNKITALKVNFQ KKKHIRRFREITLDSIDDAPTSLDCNNNLILVGCNELFNDSSMENVNHHL RKFVFEQEHLKFVASIDFNRTTDPSVFTKFVYINQRATVAAIASSEVPTV IRIIDPRNLTENYEIETGREVNDLHFAPNGILLSYITSNSLEVASVRDGN FVARKTDFDKNLVLSNIRFLNDNTLLVAASLSNSDGVSLLKLGVSSKGVK ILKTASFMFDLNGITSMDVSPNKKFVALSSNDNLVAIVSVEKLKLVQLVP RVHESTITKVTFSPDSRYLASTSMGNTINVLKLSGTSSSILRNIWKFFLN FVLLVVLAGAIQLGYKHNVHGFIYKHAHDIYKSKFKENTTIDQGSSSYFT INDDYRGITESADIISATDVASDIETEFSSFDTSTMRTTTEDEQKFVWIS SSADSQFTSADIPTSASSSSSSSSSSFYEESVTNEPIVSSPTSEITKPLA SPTEPNIVEKPSLPLNSESIDLLSSSSNSITEYPEPTPDLEEKLSSLIVE QSESEITTDRESVSKLLSTESPSLSHMPSSSSSSLSLSSSLTTSPTTALS TSTATAVTTTQTNPTNDAANTSFLDNSKPASTREIYKTKIITEVITKIEY RNIPASDSNAEAEQYVTTSSSMLLTPTDTMVSSPVSEIDPIASELERMVE TPTHSISIASEFDSVASNLIPNEEILSTSASQDSISSHPSTFSDSSITSG FQSIEVSTVTSSVLASESIPSISDSTFSKFHSISEPVSSAIVETATSSFS KTETKTSRVIAFSTEDSERSSALIDNSEYTSVLADNLEPTSVLADNSEPT SVLADSSEPTSVFTDAVQSPKTSVGQSSLSESTNIEGTSMASMIFSSSGA SIGALSDIGKGTLSVESASSTVAQPMPGVTTTAPSFVSSPHKISASSIDA SGFVQKEIMIEVQSSKDSSEAFGVRHKISENVNTPVSRMLTTEMQASGTV DVTEDVSLSSEVISALNVEITSLPNPVAPPQTIAAPLNNNSNTNIVNDDN AVAGTVNYAGLHDEL*

Protein Structures from PDB: proteins of known structure with sequence similarity to SED4/YCR067C, 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
SED4	Hardwick KG, et al. (1992) Genes that allow yeast cells to grow in the absence of the HDEL receptor. EMBO J 11(11):4187-95

Sequence Annotation Notes

Date

Note

2000-09-13

The systematic sequence was updated in the region between ORFs YCR067C and YCR068W. Note that coordinates listed below are chromosomal coordinates. Old: 235399 AATCGTAAATACATAGGCTGGGC-ATATACACTAACATGTGTCGTGACCAATGTGCAGCA 235457 ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||| New: 236665 AATCGTAAATACATAGGCTGGGCCATATACACTAACATGTGTCGTGACCAATGTGCAGCA 236724 Old: 235458 GATAGACTTGCTCATTAAATATATTCCAGGTAGGATTCTCTAAGGGTTTTTTTTTTTTCT 235517 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || New: 236725 GATAGACTTGCTCATTAAATATATTCCAGGTAGGATTCTCTAAGGGTTTTTTTTTTT-CT 236783

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
YCR067C	SGD Systematic Sequence
850431	NCBI: Gene ID
NP_009993.1	NCBI: RefSeq protein version ID
NP_009993.1	NCBI: RefSeq protein version ID
6319912	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
9 curated references; 0 references not yet curated
Reviews	Bonifacino JS and Glick BS (2004) The mechanisms of vesicle budding and fusion. Cell 116(2):153-66	|BET1 |EMP24 |EMP46 |EMP47 |ERV25 |ERV41 |GAP1 |SAR1 |SEC12 |SEC13 |SEC16 |SEC17 |SEC18 |SEC23 |MORE
Fungal Related Genes/Proteins Mapping	Payne WE, et al. (2000) Isolation of Pichia pastoris genes involved in ER-to-Golgi transport. Yeast 16(11):979-93	|SAR1 |SEC12 |SEC13 |SEC17 |SEC18
Function/Process Genetic Interactions Mutants/Phenotypes Protein Sequence Features Regulatory Role Strains/Constructs	Saito-Nakano Y and Nakano A (2000) Sed4p functions as a positive regulator of Sar1p probably through inhibition of the GTPase activation by Sec23p. Genes Cells 5(12):1039-48	|SAR1 |SEC12 |SEC16 |SEC23
Function/Process Genetic Interactions Mutants/Phenotypes Strains/Constructs	Saito Y, et al. (1999) Identification of SEC12, SED4, truncated SEC16, and EKS1/HRD3 as multicopy suppressors of ts mutants of Sar1 GTPase. J Biochem 125(1):130-7	|HMG2 |HRD3 |KAR2 |SAR1 |SEC12 |SEC16
Reviews	Kuehn MJ and Schekman R (1997) COPII and secretory cargo capture into transport vesicles. Curr Opin Cell Biol 9(4):477-83	|SAR1 |SEC23 |SEC24
Cellular Location Function/Process Fungal Related Genes/Proteins Genetic Interactions Mutants/Phenotypes Protein-protein Interactions Regulatory Role	Gimeno RE, et al. (1995) SED4 encodes a yeast endoplasmic reticulum protein that binds Sec16p and participates in vesicle formation. J Cell Biol 131(2):325-38	|SAR1 |SEC12 |SEC16
Function/Process Genetic Interactions	Nishikawa S, et al. (1994) Inhibition of endoplasmic reticulum (ER)-to-Golgi transport induces relocalization of binding protein (BiP) within the ER to form the BiP bodies. Mol Biol Cell 5(10):1129-43	|KAR2 |SEC12 |SEC17
DNA/RNA Sequence Features Mapping Mutants/Phenotypes Strains/Constructs	Benit P, et al. (1992) Sequence of the sup61-RAD18 region on chromosome III of Saccharomyces cerevisiae. Yeast 8(2):147-53	|BUD31 |HCM1 |RAD18 |SUP61
DNA/RNA Sequence Features Function/Process Fungal Related Genes/Proteins Genetic Interactions Protein Sequence Features Regulatory Role	Hardwick KG, et al. (1992) Genes that allow yeast cells to grow in the absence of the HDEL receptor. EMBO J 11(11):4187-95	|DPM1 |ERD2 |KAR2 |SEC12 |SED1

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