NEM1/YHR004C 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

ChrVIII: 113089 to 111749
CDS: 113089 - 111749

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

NEM1 YHR004C ORF, Verified S000001046

Description
Probable catalytic subunit of Nem1p-Spo7p phosphatase holoenzyme; regulates nuclear growth by controlling phospholipid biosynthesis, required for normal nuclear envelope morphology and sporulation; homolog of the human protein Dullard

GO Annotations [TOP] [NEXT]
Molecular Function
Annotation(s) Reference(s) Evidence Assigned By
hydrolase activity GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0378
Assigned on 2007-05-23 UniProtKB
phosphatase activity DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR011948
Assigned on 2007-05-23 UniProtKB
phosphoprotein phosphatase activity GOA curators and MGI curators (2001) Gene Ontology annotation based on Enzyme Commission mapping.
     IEA : Inferred from Electronic Annotation with IUBMB:3.1.3.16
Assigned on 2008-02-13 UniProtKB
GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0904
Assigned on 2008-02-14 UniProtKB
contributes_to phosphoprotein phosphatase activity Santos-Rosa H, et al. (2005) The yeast lipin Smp2 couples phospholipid biosynthesis to nuclear membrane growth. EMBO J 24(11):1931-41
         IDA : Inferred from Direct Assay
Assigned on 2009-01-26 SGD
Biological Process
Annotation(s) Reference(s) Evidence Assigned By
ascospore formation Siniossoglou S, et al. (1998) A novel complex of membrane proteins required for formation of a spherical nucleus. EMBO J 17(22):6449-64
       IMP : Inferred from Mutant Phenotype
Assigned on 2002-10-02 SGD
nuclear envelope organization Siniossoglou S, et al. (1998) A novel complex of membrane proteins required for formation of a spherical nucleus. EMBO J 17(22):6449-64
       IMP : Inferred from Mutant Phenotype
Assigned on 2009-01-26 SGD
regulation of lipid biosynthetic process Santos-Rosa H, et al. (2005) The yeast lipin Smp2 couples phospholipid biosynthesis to nuclear membrane growth. EMBO J 24(11):1931-41
         IGI : Inferred from Genetic Interaction with SGD:PAH1
Assigned on 2009-01-26 SGD
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 Siniossoglou S, et al. (1998) A novel complex of membrane proteins required for formation of a spherical nucleus. EMBO J 17(22):6449-64
       IDA : Inferred from Direct Assay
ISM : Inferred from Sequence Model
Assigned on 2002-10-02 SGD
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-9904
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
mitochondrion Sickmann A, et al. (2003) The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci U S A 100(23):13207-12
         IDA : Inferred from Direct Assay
Assigned on 2004-09-28 SGD
Reinders J, et al. (2006) Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. J Proteome Res 5(7):1543-54
           IDA : Inferred from Direct Assay
Assigned on 2006-12-12 SGD
nuclear envelope-endoplasmic reticulum network Siniossoglou S, et al. (1998) A novel complex of membrane proteins required for formation of a spherical nucleus. EMBO J 17(22):6449-64
       IDA : Inferred from Direct Assay
Assigned on 2002-10-02 SGD
nucleus GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0539
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 forNEM1/YHR004C for NEM1
1) Siniossoglou S, et al. (1998) A novel complex of membrane proteins required for formation of a spherical nucleus. EMBO J 17(22):6449-64

2) Santos-Rosa H, et al. (2005) The yeast lipin Smp2 couples phospholipid biosynthesis to nuclear membrane growth. EMBO J 24(11):1931-41

3) Kim Y, et al. (2007) A conserved phosphatase cascade that regulates nuclear membrane biogenesis. Proc Natl Acad Sci U S A 104(16):6596-601

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for NEM1/YHR004C

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for NEM1/YHR004C

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 MNALKYF

C-term EKAFNIN

Length(aa) 446

MW(Da) 50,641

pI 9.62

Amino Acid Composition (full length)

GCG tools: PepPlot, Helical Wheel, PepStruct

Transcript Translation Calculations

Codon Bias -0.055

Codon Adaptation Index 0.117

Frequency of Optimal Codons 0.377

Hydropathicity of Protein -0.475

Aromaticity Score 0.081

10 20 30 40 50 | | | | | MNALKYFSNHLITTKKQKKINVEVTKNQDLLGPSKEVSNKYTSHSENDCV SEVDQQYDHSSSHLKESDQNQERKNSVPKKPKALRSILIEKIASILWALL LFLPYYLIIKPLMSLWFVFTFPLSVIERRVKHTDKRNRGSNASENELPVS SSNINDSSEKTNPKNCNLNTIPEAVEDDLNASDEIILQRDNVKGSLLRAQ SVKSRPRSYSKSELSLSNHSSSNTVFGTKRMGRFLFPKKLIPKSVLNTQK KKKLVIDLDETLIHSASRSTTHSNSSQGHLVEVKFGLSGIRTLYFIHKRP YCDLFLTKVSKWYDLIIFTASMKEYADPVIDWLESSFPSSFSKRYYRSDC VLRDGVGYIKDLSIVKDSEENGKGSSSSLDDVIIIDNSPVSYAMNVDNAI QVEGWISDPTDTDLLNLLPFLEAMRYSTDVRNILALKHGEKAFNIN*

Protein Structures from PDB: proteins of known structure with sequence similarity to NEM1/YHR004C, based on Smith-Waterman analysis. [TOP] [NEXT]
PDB protein structure(s) homologous to NEM1 Homolog Source (per PDB) Protein Alignment: NEM1 vs. Homolog External Links
P-Value %Identical %Similar Alignment
2hhl ( Chain: C, A, D, B)
Crystal structure of the human small ctd phosphatase 3 isoform 1
PDB_Info
PDB_Structure
Homo sapiens Chain C = 1.8e-23 38 29 View alignment SCOP
MMDB
CATH
Chain A = 1.8e-23 38 29 View alignment
Chain D = 1.8e-23 38 29 View alignment
Chain B = 1.8e-23 38 29 View alignment
1t9z ( Chain: A)
Three-dimensional structure of a rna-polymerase ii binding protein.
PDB_Info
PDB_Structure
Homo sapiens 6.4e-23 35 33 View alignment SCOP
MMDB
CATH
1ta0 ( Chain: A)
Three-dimensional structure of a rna-polymerase ii binding protein with associated ligand.
PDB_Info
PDB_Structure
Homo sapiens 7.8e-23 35 33 View alignment SCOP
MMDB
CATH
2ght ( Chain: B, A)
Ctd-specific phosphatase scp1 in complex with peptide from c-terminal domain of rna polymerase ii
PDB_Info
PDB_Structure
Homo sapiens Chain B = 1.9e-22 35 33 View alignment SCOP
MMDB
CATH
Chain A = 1.9e-22 35 33 View alignment
2ghq ( Chain: A, B)
Ctd-specific phosphatase scp1 in complex with peptide c- terminal domain of rna polymerase ii
PDB_Info
PDB_Structure
Homo sapiens Chain A = 1.9e-22 35 33 View alignment SCOP
MMDB
CATH
Chain B = 1.9e-22 35 33 View alignment
2q5e ( Chain: D, E, H, F, B, G, A, C)
Crystal structure of human carboxy-terminal domain rna polymerase ii polypeptide a small phosphatase 2
PDB_Info
PDB_Structure
Homo sapiens Chain D = 2.0e-22 35 31 View alignment SCOP
MMDB
CATH
Chain E = 2.0e-22 35 31 View alignment
Chain H = 2.0e-22 35 31 View alignment
Chain F = 2.0e-22 35 31 View alignment
Chain B = 2.0e-22 35 31 View alignment
Chain G = 2.0e-22 35 31 View alignment
Chain A = 2.0e-22 35 31 View alignment
Chain C = 2.0e-22 35 31 View alignment
3ef0 ( Chain: A)
The structure of fcp1, an essential rna polymerase ii ctd phosphatase
PDB_Info
PDB_Structure
Schizosaccharomyces pombe 0.002200 30 27 View alignment SCOP
MMDB
CATH
3ef1 ( Chain: A)
The structure of fcp1, an essential rna polymerase ii ctd phosphatase
PDB_Info
PDB_Structure
Schizosaccharomyces pombe 0.002800 30 27 View alignment SCOP
MMDB
CATH

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
NEM1 Siniossoglou S, et al. (1998) A novel complex of membrane proteins required for formation of a spherical nucleus. EMBO J 17(22):6449-64

Standard Name	Reference
NEM1	*Siniossoglou S, et al.* (1998)** A novel complex of membrane proteins required for formation of a spherical nucleus. EMBO J 17(22):6449-64

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

YHR004C SGD Systematic Sequence

856393 NCBI: Gene ID

NP_011867.1 NCBI: RefSeq protein version ID

NP_011867.1 NCBI: RefSeq protein version ID

6321791 NCBI: NCBI protein GI

Sequence from other databases
Sequence ID	Source
YHR004C	SGD Systematic Sequence
856393	NCBI: Gene ID
NP_011867.1	NCBI: RefSeq protein version ID
NP_011867.1	NCBI: RefSeq protein version ID
6321791	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
18 curated references; 0 references not yet curated
Genetic Interactions
Mutants/Phenotypes
Hodg CA, et al. (2010) Integral membrane proteins Brr6 and Apq12 link assembly of the nuclear pore complex to lipid homeostasis in the endoplasmic reticulum. J Cell Sci 123(Pt 1):141-151
       |ACC1 |APQ12 |ARE1 |ARE2 |ARV1 |BRR6 |DGA1 |ELO1 |ERG2 |ERG3 |ERG4 |ERG5 |ERG6 |FEN1 |MORE
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Dawson TR, et al. (2009) ER membrane-bending proteins are necessary for de novo nuclear pore formation. J Cell Biol 184(5):659-75
       |GLE2 |NIC96 |NUP116 |NUP120 |NUP133 |NUP145 |NUP188 |NUP49 |NUP82 |NUP84 |NUP85 |POM152 |POM34 |RTN1 |MORE
Genetic Interactions
Federovitch CM, et al. (2008) Genetic and structural analysis of Hmg2p-induced endoplasmic reticulum remodeling in Saccharomyces cerevisiae. Mol Biol Cell 19(10):4506-20
       |BNI1 |BNR1 |CHO2 |ERG28 |ERV25 |HER1 |HER2 |HMG1 |HMG2 |HOF1 |HRD1 |KAR2 |OPI3 |PSD1 |MORE
Genetic Interactions
Han GS, et al. (2008) An unconventional diacylglycerol kinase that regulates phospholipid synthesis and nuclear membrane growth. J Biol Chem 283(29):20433-42
       |CDS1 |CHO2 |DGK1 |GAT2 |OPI3 |PAH1 |PSD1 |SPO7
Computational analysis
Mutants/Phenotypes
Protein-protein Interactions
Schluter C, et al. (2008) Global Analysis of Yeast Endosomal Transport Identifies the Vps55/68 Sorting Complex. Mol Biol Cell 19(4):1282-1294
       |AKR1 |ARF1 |ARP5 |ARP6 |BRO1 |BUD32 |CDC50 |COG5 |COG6 |COG7 |COG8 |CUP5 |DID4 |EAF1 |MORE
Cellular Location
Cross-species Expression
Function/Process
Mutants/Phenotypes
Non-Fungal Related Genes/Proteins
Protein Sequence Features
Strains/Constructs
Substrates/Ligands/Cofactors
Kim Y, et al. (2007) A conserved phosphatase cascade that regulates nuclear membrane biogenesis. Proc Natl Acad Sci U S A 104(16):6596-601

Mutants/Phenotypes
Substrates/Ligands/Cofactors
O'Hara L, et al. (2006) Control of phospholipid synthesis by phosphorylation of the yeast lipin Pah1p/Smp2p Mg2+-dependent phosphatidate phosphatase. J Biol Chem 281(45):34537-48
       |INO1 |OPI1 |OPI3 |PAH1 |SPO7
Cellular Location
Reinders J, et al. (2006) Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. J Proteome Res 5(7):1543-54
           |AAC1 |AAC3 |AAT1 |ABC1 |ABF2 |ACC1 |ACH1 |ACK1 |ACN9 |ACO1 |ACO2 |ACP1 |ACS1 |ADH3 |MORE
Function/Process
Genetic Interactions
Mutants/Phenotypes
Protein Sequence Features
Regulatory Role
Strains/Constructs
Substrates/Ligands/Cofactors
Santos-Rosa H, et al. (2005) The yeast lipin Smp2 couples phospholipid biosynthesis to nuclear membrane growth. EMBO J 24(11):1931-41
         |CDC28 |PAH1 |SPO7
Genetic Interactions
Strains/Constructs
Tong AH, et al. (2004) Global mapping of the yeast genetic interaction network. Science 303(5659):808-13
           |AAD4 |AAH1 |ABF2 |ACE2 |ADH6 |AEP2 |AFG1 |AGP1 |AHC1 |AHC2 |AIM21 |AIM22 |AIM26 |AIM29 |MORE
Function/Process
Mutants/Phenotypes
Strains/Constructs
Enyenihi AH and Saunders WS (2003) Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae. Genetics 163(1):47-54
           |ADA2 |ADY2 |AKR1 |APS3 |APT1 |ARC1 |ARG82 |ARO2 |ATF1 |ATG11 |ATG15 |ATG16 |ATG5 |BPH1 |MORE
Mutants/Phenotypes
Strains/Constructs
Kushner DB, et al. (2003) Systematic, genome-wide identification of host genes affecting replication of a positive-strand RNA virus. Proc Natl Acad Sci U S A 100(26):15764-9
           |ACB1 |ALF1 |AML1 |BRO1 |BUB1 |BUD26 |BUD31 |CBC2 |CDC50 |DBR1 |DED1 |DHH1 |DOA1 |DOA4 |MORE
Cellular Location
Sickmann A, et al. (2003) The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci U S A 100(23):13207-12
         |AAC1 |AAC3 |AAT1 |ABC1 |ABF2 |ACC1 |ACH1 |ACK1 |ACO1 |ACO2 |ACP1 |ACS1 |ADH3 |ADK2 |MORE
Mutants/Phenotypes
Strains/Constructs
Fleming JA, et al. (2002) Complementary whole-genome technologies reveal the cellular response to proteasome inhibition by PS-341. Proc Natl Acad Sci U S A 99(3):1461-6
             |APN1 |ATG17 |BEM4 |BIK1 |CCR4 |CDC26 |CHL1 |CHL4 |CLB2 |CLB5 |CSM3 |CTF19 |CTF8 |DCC1 |MORE
RNA Levels and Processing
Regulation of
Lombardia LJ, et al. (2002) Genome-wide analysis of yeast transcription upon calcium shortage. Cell Calcium 32(2):83-91
               |ANR2 |APP1 |ARC40 |BAP3 |BDF1 |BIO4 |CDC14 |CDC24 |CDC6 |CHS6 |CIS3 |CPA1 |CPA2 |CSM3 |MORE
Fungal Related Genes/Proteins
Siniossoglou S, et al. (2000) Psr1p/Psr2p, two plasma membrane phosphatases with an essential DXDX(T/V) motif required for sodium stress response in yeast. J Biol Chem 275(25):19352-60
       |ENA1 |PSR1 |PSR2
Cellular Location
Genetic Interactions
Mutants/Phenotypes
Strains/Constructs
Siniossoglou S, et al. (1998) A novel complex of membrane proteins required for formation of a spherical nucleus. EMBO J 17(22):6449-64
       |NUP84 |SPO7
Alias
Non-Fungal Related Genes/Proteins
Su YA, et al. (1997) Characterization of a highly conserved gene (OS4) amplified with CDK4 in human sarcomas. Oncogene 15(11):1289-94
     |PSR1 |PSR2 |TIM50

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