PBN1/YCL052C 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: 35393 to 34143
CDS: 35393 - 34143

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

PBN1 YCL052C ORF, Verified S000000557

Description
Essential component of glycosylphosphatidylinositol-mannosyltransferase I, required for the autocatalytic post-translational processing of the protease B precursor Prb1p, localizes to ER in lumenal orientation; homolog of mammalian PIG-X

GO Annotations [TOP] [NEXT]
Molecular Function
Annotation(s) Reference(s) Evidence Assigned By
contributes_to mannosyltransferase activity Ashida H, et al. (2005) Mammalian PIG-X and yeast Pbn1p are the essential components of glycosylphosphatidylinositol-mannosyltransferase I. Mol Biol Cell 16(3):1439-48
       IMP : Inferred from Mutant Phenotype
Assigned on 2005-02-10 SGD
Biological Process
Annotation(s) Reference(s) Evidence Assigned By
ER-associated protein catabolic process Subramanian S, et al. (2006) Pbn1p: an essential endoplasmic reticulum membrane protein required for protein processing in the endoplasmic reticulum of budding yeast. Proc Natl Acad Sci U S A 103(4):939-44
       IMP : Inferred from Mutant Phenotype
Assigned on 2006-11-02 SGD
GPI anchor biosynthetic process Ashida H, et al. (2005) Mammalian PIG-X and yeast Pbn1p are the essential components of glycosylphosphatidylinositol-mannosyltransferase I. Mol Biol Cell 16(3):1439-48
       IMP : Inferred from Mutant Phenotype
Assigned on 2005-02-10 SGD
DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR013233
Assigned on 2008-10-13 UniProtKB
GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0337
Assigned on 2007-05-23 UniProtKB
protein processing Naik RR and Jones EW (1998) The PBN1 gene of Saccharomyces cerevisiae: an essential gene that is required for the post-translational processing of the protease B precursor. Genetics 149(3):1277-92
       IMP : Inferred from Mutant Phenotype
Assigned on 2002-07-11 SGD
Cellular Component
Annotation(s) Reference(s) Evidence Assigned By
endoplasmic reticulum Naik RR and Jones EW (1998) The PBN1 gene of Saccharomyces cerevisiae: an essential gene that is required for the post-translational processing of the protease B precursor. Genetics 149(3):1277-92
       IDA : Inferred from Direct Assay
Assigned on 2002-07-11 SGD
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
endoplasmic reticulum membrane DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR013233
Assigned on 2009-06-17 UniProtKB
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-9907
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]
No summary paragraph available

Basic References [TOP]
BASIC INFORMATION REFERENCES forPBN1/YCL052C for PBN1
1) Naik RR and Jones EW (1998) The PBN1 gene of Saccharomyces cerevisiae: an essential gene that is required for the post-translational processing of the protease B precursor. Genetics 149(3):1277-92

2) Ashida H, et al. (2005) Mammalian PIG-X and yeast Pbn1p are the essential components of glycosylphosphatidylinositol-mannosyltransferase I. Mol Biol Cell 16(3):1439-48

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for PBN1/YCL052C

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for PBN1/YCL052C

Homologs [TOP] [NEXT]

Comparison Resources

Physical Properties and Transcript Information: predicted from sequence [TOP] [NEXT]
Protein Sequence Calculations
from Predicted Full length Translation

N-term MVTRHRV

C-term KRSVKRE

Length(aa) 416

MW(Da) 47,923

pI 5.44

Amino Acid Composition (full length)

GCG tools: PepPlot, Helical Wheel, PepStruct

Transcript Translation Calculations

Codon Bias 0.012

Codon Adaptation Index 0.132

Frequency of Optimal Codons 0.414

Hydropathicity of Protein -0.462

Aromaticity Score 0.099

10 20 30 40 50 | | | | | MVTRHRVTVLYNAPEDIGNHMRQNDTHLTVRGGSGVVLQQRWLLERTGSL DKSFTRITWRPRADLARSLSVIENELSAGFSVYSNSSDVPERFITNPVYN SFHSEKFDIEQYLPPEVDLNLSWNPEDFTYDISVEPTQIQIVEYRLLKQG EEFTIARVKDEKLEVGVFFVDASDESDVDIGGIRCNWRMDDGKMERCQKT SLLYKQGHIAYNHSTTTTSLYLNEPIGLHPKIMIDLTDFEERPKCMYLMH LQLPLELFIDKFQSSPLLLFGEDDLELPEYSLRDKAWGSESIFELKAGTM NEVTLHTRYIEPSNNKGDKLEVSFDPEVILACDTGDNKVSRNPFYKKGLG YESLFTDDTTFRHLNSTTLLVPIPRPDTKDYSKIKNGTLLCLLISIIYIF SKVFGNNKKKRSVKRE*

Protein Structures from PDB: proteins of known structure with sequence similarity to PBN1/YCL052C, based on Smith-Waterman analysis. [TOP] [NEXT]
No protein structure information available.

Genome-wide Expression and Other Large-Scale Analyses [TOP] [NEXT]

Functional Analysis
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
PBN1 Naik RR and Jones EW (1998) The PBN1 gene of Saccharomyces cerevisiae: an essential gene that is required for the post-translational processing of the protease B precursor. Genetics 149(3):1277-92

Sequence Annotation Notes
Date Note
2000-09-13 Four single nucleotide insertions were made in the systematic sequence in the intergenic region between ORFs YCL052C and YCL051W. Note that coordinates listed are chromosomal coordinates.
Old: 35450 TGATCTTTTTTATCAGGGGGATCTTCAAAGAAAGGAACTTTTTTTAGGAAAAAAAAA-TA 35508 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || New: 35467 TGATCTTTTTTATCAGGGGGATCTTCAAAGAAAGGAACTTTTTTTAGGAAAAAAAAAATA 35526

Old: 35569 -GT-CTGCTGT-AGTGTGTCCTCCAATACTCTTGCACGACAAAGTTTTAGTTATCCCCTT 35625 || ||||||| |||||||||||||||||||||||||||||||||||||||||||||||| New: 35587 AGTTCTGCTGTTAGTGTGTCCTCCAATACTCTTGCACGACAAAGTTTTAGTTATCCCCTT 35646

Standard Name	Reference
PBN1	Naik RR and Jones EW (1998) The PBN1 gene of Saccharomyces cerevisiae: an essential gene that is required for the post-translational processing of the protease B precursor. Genetics 149(3):1277-92

Date	Note
2000-09-13	Four single nucleotide insertions were made in the systematic sequence in the intergenic region between ORFs YCL052C and YCL051W. Note that coordinates listed are chromosomal coordinates. Old: 35450 TGATCTTTTTTATCAGGGGGATCTTCAAAGAAAGGAACTTTTTTTAGGAAAAAAAAA-TA 35508 \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\| \|\| New: 35467 TGATCTTTTTTATCAGGGGGATCTTCAAAGAAAGGAACTTTTTTTAGGAAAAAAAAAATA 35526 Old: 35569 -GT-CTGCTGT-AGTGTGTCCTCCAATACTCTTGCACGACAAAGTTTTAGTTATCCCCTT 35625 \|\| \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\| New: 35587 AGTTCTGCTGTTAGTGTGTCCTCCAATACTCTTGCACGACAAAGTTTTAGTTATCCCCTT 35646

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
Sequence from other databases

Sequence ID Source

YCL052C SGD Systematic Sequence

850305 NCBI: Gene ID

NP_009878.1 NCBI: RefSeq protein version ID

NP_009878.1 NCBI: RefSeq protein version ID

6319797 NCBI: NCBI protein GI

Sequence from other databases
Sequence ID	Source
YCL052C	SGD Systematic Sequence
850305	NCBI: Gene ID
NP_009878.1	NCBI: RefSeq protein version ID
NP_009878.1	NCBI: RefSeq protein version ID
6319797	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

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

Literature Guide: papers categorized by topic. [TOP]
Topics Reference Other Genes Addressed
14 curated references; 0 references not yet curated
Strains/Constructs
Techniques and Reagents
Flagfeldt DB, et al. (2009) Characterization of chromosomal integration sites for heterologous gene expression in Saccharomyces cerevisiae. Yeast 26(10):545-51
       |PDC6 |SPB1 |URA3 |YARCdelta8 |YBRWdelta16 |YCRWdelta11 |YCRWdelta12 |YDRWdelta31 |YERCdelta8 |YGLCtau3 |YGLWdelta4 |YHRCdelta14 |YIRCdelta6 |YMRWdelta15 |MORE
Reviews
Fujita M and Kinoshita T (2009) Structural remodeling of GPI anchors during biosynthesis and after attachment to proteins. FEBS Lett
     |ARV1 |BST1 |CDC1 |CWH43 |ERI1 |GAA1 |GAB1 |GPI1 |GPI10 |GPI11 |GPI12 |GPI13 |GPI14 |GPI15 |MORE
Mutants/Phenotypes
Strains/Constructs
Breslow DK, et al. (2008) A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nat Methods 5(8):711-8
       |AAR2 |ABD1 |ABF1 |ACC1 |ACP1 |ADE13 |AFG2 |ALA1 |ALG1 |ALG13 |ALG14 |ALG2 |ALG7 |ALR1 |MORE
Reviews
Bosson R and Conzelmann A (2007) Multiple functions of inositolphosphorylceramides in the formation and intracellular transport of glycosylphosphatidylinositol-anchored proteins in yeast. Biochem Soc Symp (74):199-209
     |BST1 |ERI1 |GAA1 |GAB1 |GPI1 |GPI10 |GPI11 |GPI12 |GPI13 |GPI14 |GPI15 |GPI16 |GPI17 |GPI18 |MORE
Non-Fungal Related Genes/Proteins
Kim YU, et al. (2007) Both mammalian PIG-M and PIG-X are required for growth of GPI14-disrupted yeast. J Biochem 142(1):123-9
       |GPI14
Reviews
Orlean P and Menon AK (2007) Thematic review series: lipid posttranslational modifications. GPI anchoring of protein in yeast and mammalian cells, or: how we learned to stop worrying and love glycophospholipids. J Lipid Res 48(5):993-1011
         |BST1 |CWH43 |ERI1 |GAA1 |GAB1 |GPI1 |GPI10 |GPI11 |GPI12 |GPI13 |GPI14 |GPI15 |GPI16 |GPI17 |MORE
Reviews
Pittet M and Conzelmann A (2007) Biosynthesis and function of GPI proteins in the yeast Saccharomyces cerevisiae. Biochim Biophys Acta 1771(3):405-20
       |BST1 |CWH43 |ERI1 |GAA1 |GAB1 |GPI1 |GPI10 |GPI11 |GPI12 |GPI13 |GPI14 |GPI15 |GPI16 |GPI17 |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
Function/Process
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Subramanian S, et al. (2006) Pbn1p: an essential endoplasmic reticulum membrane protein required for protein processing in the endoplasmic reticulum of budding yeast. Proc Natl Acad Sci U S A 103(4):939-44
       |CNE1 |ERO1 |GAS1 |PHO8 |PRB1
Cross-species Expression
Function/Process
Non-Fungal Related Genes/Proteins
Strains/Constructs
Substrates/Ligands/Cofactors
Ashida H, et al. (2005) Mammalian PIG-X and yeast Pbn1p are the essential components of glycosylphosphatidylinositol-mannosyltransferase I. Mol Biol Cell 16(3):1439-48
       |GPI14
DNA/RNA Sequence Features
Fungal Related Genes/Proteins
Zhou Z, et al. (2001) A Saccharomyces servazzii clone homologous to Saccharomyces cerevisiae chromosome III spanning KAR4, ARS 304 and SPB1 lacks the recombination enhancer but contains an unknown ORF. Yeast 18(9):789-95
     |ARS304 |KAR4 |PRD1 |SPB1
Cellular Location
DNA/RNA Sequence Features
Function/Process
Mutants/Phenotypes
Protein Sequence Features
Strains/Constructs
Techniques and Reagents
Naik RR and Jones EW (1998) The PBN1 gene of Saccharomyces cerevisiae: an essential gene that is required for the post-translational processing of the protease B precursor. Genetics 149(3):1277-92
       |PRB1
Alias
Genetic Interactions
Strains/Constructs
Lai MH, et al. (1997) Multiple copies of PBS2, MHP1 or LRE1 produce glucanase resistance and other cell wall effects in Saccharomyces cerevisiae. Yeast 13(3):199-213
       |FKS1 |LRE1 |MHP1 |PBS2
Mutants/Phenotypes
Strains/Constructs
Rieger KJ, et al. (1997) Large-scale phenotypic analysis--the pilot project on yeast chromosome III. Yeast 13(16):1547-62
       |BPH1 |BUD23 |CSM1 |CTR86 |CWH43 |FEN1 |IMG1 |IMG2 |KRR1 |MRPL32 |NFS1 |RRP7 |RSA4 |SAT4 |MORE

Return to SGD

SGD^tm pages Database Copyright © 1997-2010 The Board of Trustees of Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied. The SGD project at Stanford University is supported by a Genome Research Resource Grant from the US National Human Genome Research Institute, part of the US National Institutes of Health.