SpermatogenesisOnline 1.0

Tag Content
SG ID
SG00011566 
UniProt Accession
Theoretical PI
9.07  
Molecular Weight
93246 Da  
Genbank Nucleotide ID
Genbank Protein ID
Gene Name
Stt3b 
Gene Synonyms/Alias
Simp 
Protein Name
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3B 
Protein Synonyms/Alias
Oligosaccharyl transferase subunit STT3BSTT3-BEC=2.4.1.119 B6dom1 antigen; Source of immunodominant MHC-associated peptides; 
Organism
Mus musculus (Mouse) 
NCBI Taxonomy ID
10090 
Chromosome Location
chr:9;115151725-115219539;-1
View in Ensembl genome browser  
Function in Stage
Uncertain 
Function in Cell Type
Uncertain 
Probability (GAS) of Function in Spermatogenesis
0.76495486 
The probability was calculated by GAS algorithm, ranging from 0 to 1. The closer it is to 1, the more possibly it functions in spermatogenesis.
Description
Temporarily unavailable 
Abstract of related literatures
1. This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development. PMID: [16141072] 

2. The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5'-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline. PMID: [15489334] 

3. The B6(dom1) minor histocompatibility antigen (MiHA) is a model antigen, since it is both the epitome of an immunodominant epitope and an ideal target for adoptive cancer immunotherapy. Based on DNA sequencing and MS/MS analyses, we report that B6(dom1) corresponds to amino acids 770-778 (KAPDNRETL) of a protein we propose to call SIMP (source of immunodominant MHC-associated peptides) that is encoded by a mouse homolog of the yeast STT3gene. STT3, a member of the oligosaccharyltransferase complex, is essential for cell proliferation. Phenotypic and genotypic analyses among eight strains of mice revealed a precise correlation between susceptibility or resistance to B6(dom1)-specific cytotoxic T lymphocytes (CTLs) and the presence of a Glu vs Asp amino acid at position 776 of the SIMP protein, respectively. Strikingly, while the difference in the amino acid sequence 770-778 encoded by the two SIMP alleles represents a very conservative substitution, these allelic peptides were not crossreactive at the CTL level, and both peptides were immunodominant when presented to mice homozygous for the opposite allele. In addition, we have cloned a human ortholog of SIMP whose predicted protein shares 97% amino acid identity with mouse SIMP. These results strengthen the concept that MHC class-I-associated MiHAs originate as a consequence of rare polymorphisms among highly conserved genes. Furthermore, the notion that a peptide differing from a self analog by a single methylene group can be immunodominant has implications regarding our understanding of the mechanisms of immunodominance. PMID: [12439619] 

4. A system which consisted of multidimensional liquid chromatography (Yin-yang MDLC) coupled with mass spectrometry was used for the identification of peptides and phosphopeptides. The multidimensional liquid chromatography combines the strong-cation exchange (SCX), strong-anion exchange (SAX), and reverse-phase methods for the separation. Protein digests were first loaded on an SCX column. The flow-through peptides from SCX were collected and further loaded on an SAX column. Both columns were eluted by offline pH steps, and the collected fractions were identified by reverse-phase liquid chromatography tandem mass spectrometry. Comprehensive peptide identification was achieved by the Yin-yang MDLC-MS/MS for a 1 mg mouse liver. In total, 14 105 unique peptides were identified with high confidence, including 13 256 unmodified peptides and 849 phosphopeptides with 809 phosphorylated sites. The SCX and SAX in the Yin-Yang system displayed complementary features of binding and separation for peptides. When coupled with reverse-phase liquid chromatography mass spectrometry, the SAX-based method can detect more extremely acidic (pI < 4.0) and phosphorylated peptides, while the SCX-based method detects more relatively basic peptides (pI > 4.0). In total, 134 groups of phosphorylated peptide isoforms were obtained, with common peptide sequences but different phosphorylated states. This unbiased profiling of protein expression and phosphorylation provides a powerful approach to probe protein dynamics, without using any prefractionation and chemical derivation. PMID: [17203969] 

5. External stimuli trigger internal signaling events within a cell that may represent either a temporary or permanent shift in the phosphorylation state of its proteome. Numerous reports have elucidated phosphorylation sites from a variety of biological samples and more recent studies have monitored the temporal dynamics of protein phosphorylation as a given system is perturbed. Understanding which proteins are phosphorylated as well as when they are phosphorylated may indicate novel functional roles within a system and allow new therapeutic avenues to be explored. To elucidate the dynamics of protein phosphorylation within differentiating murine P19 embryonal carcinoma cells, we induced P19 cells to differentiate using all-trans-retinoic acid and developed a strategy that combines isotopically labeled methyl esterification, immobilized metal affinity chromatography, mass spectrometric analysis, and a rigorous and unique data evaluation approach. We present the largest differential phosphoproteomic analysis using isotopically labeled methyl esterification to date, identifying a total of 472 phosphorylation sites on 151 proteins; 56 of these proteins had altered abundances following treatment with retinoic acid and approximately one-third of these have been previously associated with cellular differentiation. A series of bioinformatic tools were used to extract information from the data and explore the implications of our findings. This study represents the first global gel-free analysis that elucidates protein phosphorylation dynamics during cellular differentiation. PMID: [17622165] 

6. Protein phosphorylation is a complex network of signaling and regulatory events that affects virtually every cellular process. Our understanding of the nature of this network as a whole remains limited, largely because of an array of technical challenges in the isolation and high-throughput sequencing of phosphorylated species. In the present work, we demonstrate that a combination of tandem phosphopeptide enrichment methods, high performance MS, and optimized database search/data filtering strategies is a powerful tool for surveying the phosphoproteome. Using our integrated analytical platform, we report the identification of 5,635 nonredundant phosphorylation sites from 2,328 proteins from mouse liver. From this list of sites, we extracted both novel and known motifs for specific Ser/Thr kinases including a "dipolar" motif. We also found that C-terminal phosphorylation was more frequent than at any other location and that the distribution of potential kinases for these sites was unique. Finally, we identified double phosphorylation motifs that may be involved in ordered phosphorylation. PMID: [17242355] 

7. Kinases play a prominent role in tumor development, pointing to the presence of specific phosphorylation patterns in tumor tissues. Here, we investigate whether recently developed high resolution mass spectrometric (MS) methods for proteome and phosphoproteome analysis can also be applied to solid tumors. As tumor model, we used TG3 mutant mice carrying skin melanomas. At total of 100 microg of solid tumor lysate yielded a melanoma proteome of 4443 identified proteins, including at least 88 putative melanoma markers previously found by cDNA microarray technology. Analysis of 2 mg of lysate from dissected melanoma with titansphere chromatography and 8 mg with strong cation exchange together resulted in the identification of more than 5600 phosphorylation sites on 2250 proteins. The phosphoproteome included many hits from pathways important in melanoma. One-month storage at -80 degrees C did not significantly decrease the number of identified phosphorylation sites. Thus, solid tumor can be analyzed by MS-based proteomics with similar efficiency as cell culture models and in amounts compatible with biopsies. PMID: [19367708] 

8. We used on-line electron capture dissociation (ECD) for the large scale identification and localization of sites of phosphorylation. Each FT-ICR ECD event was paired with a linear ion trap collision-induced dissociation (CID) event, allowing a direct comparison of the relative merits of ECD and CID for phosphopeptide identification and site localization. Linear ion trap CID was shown to be most efficient for phosphopeptide identification, whereas FT-ICR ECD was superior for localization of sites of phosphorylation. The combination of confident CID and ECD identification and confident CID and ECD localization is particularly valuable in cases where a phosphopeptide is identified just once within a phosphoproteomics experiment. PMID: [19131326] 

9. Although the classification of cell types often relies on the identification of cell surface proteins as differentiation markers, flow cytometry requires suitable antibodies and currently permits detection of only up to a dozen differentiation markers in a single measurement. We use multiplexed mass-spectrometric identification of several hundred N-linked glycosylation sites specifically from cell surface-exposed glycoproteins to phenotype cells without antibodies in an unbiased fashion and without a priori knowledge. We apply our cell surface-capturing (CSC) technology, which covalently labels extracellular glycan moieties on live cells, to the detection and relative quantitative comparison of the cell surface N-glycoproteomes of T and B cells, as well as to monitor changes in the abundance of cell surface N-glycoprotein markers during T-cell activation and the controlled differentiation of embryonic stem cells into the neural lineage. A snapshot view of the cell surface N-glycoproteins will enable detection of panels of N-glycoproteins as potential differentiation markers that are currently not accessible by other means. PMID: [19349973] 

Back to Top
Function
Component of the N-oligosaccharyl transferase enzymewhich catalyzes the transfer of a high mannose oligosaccharidefrom a lipid-linked oligosaccharide donor to an asparagine residuewithin an Asn-X-Ser/Thr consensus motif in nascent polypeptidechains. N-glycosylation occurs cotranslationally and the complexassociates with the Sec61 complex at the channel-formingtranslocon complex that mediates protein translocation across theendoplasmic reticulum (ER). SST3B seems to be involved in complexsubstrate specificity (By similarity). 
Back to Top
Subcellular Location
Endoplasmic reticulum membrane; Multi-passmembrane protein. 
Tissue Specificity
 
Gene Ontology
GO IDGO termEvidence
GO:0016021 C:integral to membrane IEA:UniProtKB-KW.
GO:0008250 C:oligosaccharyltransferase complex ISS:UniProtKB.
GO:0004579 F:dolichyl-diphosphooligosaccharide-protein glycotransferase activity IEA:EC.
GO:0018279 P:protein N-linked glycosylation via asparagine ISS:UniProtKB.
Back to Top
Interpro
IPR003674;    Oligo_trans_STT3.
Back to Top
Pfam
PF02516;    STT3;    1.
Back to Top
SMART
PROSITE
PRINTS
Created Date
18-Oct-2012 
Record Type
GAS predicted 
Sequence Annotation
INIT_MET      1      1       Removed (By similarity).
CHAIN         2    823       Dolichyl-diphosphooligosaccharide--
                             protein glycosyltransferase subunit
                             STT3B.
                             /FTId=PRO_0000246002.
TRANSMEM     62     82       Helical; (Potential).
TRANSMEM    134    154       Helical; (Potential).
TRANSMEM    166    186       Helical; (Potential).
TRANSMEM    189    209       Helical; (Potential).
TRANSMEM    240    256       Helical; (Potential).
TRANSMEM    260    280       Helical; (Potential).
TRANSMEM    289    309       Helical; (Potential).
TRANSMEM    317    337       Helical; (Potential).
TRANSMEM    348    368       Helical; (Potential).
TRANSMEM    408    428       Helical; (Potential).
TRANSMEM    438    458       Helical; (Potential).
TRANSMEM    461    481       Helical; (Potential).
TRANSMEM    535    555       Helical; (Potential).
MOD_RES       2      2       N-acetylalanine (By similarity).
MOD_RES      18     18       Phosphoserine (By similarity).
MOD_RES      29     29       Phosphoserine (By similarity).
MOD_RES     495    495       Phosphoserine.
MOD_RES     496    496       Phosphoserine.
CARBOHYD    624    624       N-linked (GlcNAc...).
CARBOHYD    638    638       N-linked (GlcNAc...).
VARIANT     776    776       E -> D (in strain: A.BY, B10.H7 and
                             C3H.SW; correlated with B6dom1-negative
                             phenotype).
CONFLICT     43     43       S -> R (in Ref. 1; BAE41550 and 2;
                             AAH03206).
CONFLICT    240    240       T -> I (in Ref. 1; BAE41550).
CONFLICT    294    294       F -> L (in Ref. 1; BAB31390).
Back to Top
Nucleotide Sequence
Length: 2709 bp   Go to nucleotide: FASTA
Protein Sequence
Length: 823 bp   Go to amino acid: FASTA
The verified Protein-Protein interaction information
UniProt
 Gene Symbol Ref Databases
Psen1IntAct 
Other Protein-Protein interaction resources
String database  
View Microarray data
Comments