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Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF THE YEAST SIR3 BAH DOMAIN

Authors :   R. M. Xu

Date :   31 Jan 06 (Deposition) - 05 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Mainly Beta, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. J. Connelly, P. Yuan, H. C. Hsu, Z. Li, R. M. Xu, R. Sternglanz
Structure And Function Of The Saccharomyces Cerevisiae Sir3 Bah Domain.
Mol. Cell. Biol. V. 26 3256 2006
PubMed-ID: 16581798 | Reference-DOI: 10.1128/MCB.26.8.3256-3265.2006
(for further references see the PDB file header)

Molecule 1 - REGULATORY PROTEIN SIR3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	BAH DOMAIN
	Gene	:	SIR3
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	SILENT INFORMATION REGULATOR 3

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2FVU)

(no "Site" information available for 2FVU)

(no "SS Bond" information available for 2FVU)

(no "Cis Peptide Bond" information available for 2FVU)

(no "SAP(SNP)/Variant" information available for 2FVU)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BAH	PS51038	BAH domain profile.	SIR3_YEAST	48-188	2	A:48-188 B:48-188

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YLR442C	1	YLR442C.1	XII:1022248-1019312	2937	SIR3_YEAST	1-978	978	2	A:1-213 (gaps) B:1-213 (gaps)	213 213

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:190
 aligned with SIR3_YEAST | P06701 from UniProtKB/Swiss-Prot  Length:978

    Alignment length:216
                               1                                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207      
           SIR3_YEAST     - ---MAKTLKDLDGWQVIITDDQGRVIDDNNRRRSRKRGGENVFLKRISDGLSFGKGESVIFNDNVTETYSVYLIHEIRLNTLNNVVEIWVFSYLRWFELKPKLYYEQFRPDLIKEDHPLEFYKDKFFNEVNKSELYLTAELSEIWLKDFIAVGQILPESQWNDSSIDKIEDRDFLVRYACEPTAEKFVPIDIFQIIRRVKEMEPKQSDEYLKRVSV 213
               SCOP domains d2fvua_ A: automated                     matches                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee......eeeeee.--------------------.eeeee.....eee...eeeeee....eeeeeeeeeee.------.eeeeeeeehhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...eeeeeeeeeeehhh.eeee.eeehhhhhh..........eeeeeee........ee.hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------BAH  PDB: A:48-188 UniProt: 48-188                                                                                                           ------------------------- PROSITE
               Transcript 1 ---Exon 1.1  PDB: A:1-213 (gaps) UniProt: 1-978 [INCOMPLETE]                                                                                                                                                             Transcript 1
                 2fvu A  -2 HMTMAKTLKDLDGWQVIITD--------------------NVFLKRISDGLSFGKGESVIFNDNVTETYSVYLIHEIRL------VEIWVFSYLRWFELKPKLYYEQFRPDLIKEDHPLEFYKDKFFNEVNKSELYLTAELSEIWLKDFIAVGQILPESQWNDSSIDKIEDRDFLVRYACEPTAEKFVPIDIFQIIRRVKEMEPKQSDEYLKRVSV 213
                                     7        17         -         -|       47        57        67        |-     |  87        97       107       117       127       137       147       157       167       177       187       197       207      
                                              17                   38                                    76     83

Chain B from PDB  Type:PROTEIN  Length:191
 aligned with SIR3_YEAST | P06701 from UniProtKB/Swiss-Prot  Length:978

    Alignment length:216
                               1                                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207      
           SIR3_YEAST     - ---MAKTLKDLDGWQVIITDDQGRVIDDNNRRRSRKRGGENVFLKRISDGLSFGKGESVIFNDNVTETYSVYLIHEIRLNTLNNVVEIWVFSYLRWFELKPKLYYEQFRPDLIKEDHPLEFYKDKFFNEVNKSELYLTAELSEIWLKDFIAVGQILPESQWNDSSIDKIEDRDFLVRYACEPTAEKFVPIDIFQIIRRVKEMEPKQSDEYLKRVSV 213
               SCOP domains d2fvub_ B: automated                    matches                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee......eeeeee.-------------------.eeeeee.....eee...eeeee......eeeeeeeeee.------.eeeeeeeehhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...eeeeeeeeeeehhh.eeee.eeehhhhhh..........eeeeeee........ee.hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------BAH  PDB: B:48-188 UniProt: 48-188                                                                                                           ------------------------- PROSITE
               Transcript 1 ---Exon 1.1  PDB: B:1-213 (gaps) UniProt: 1-978 [INCOMPLETE]                                                                                                                                                             Transcript 1
                 2fvu B  -2 HMTMAKTLKDLDGWQVIITD-------------------ENVFLKRISDGLSFGKGESVIFNDNVTETYSVYLIHEIRL------VEIWVFSYLRWFELKPKLYYEQFRPDLIKEDHPLEFYKDKFFNEVNKSELYLTAELSEIWLKDFIAVGQILPESQWNDSSIDKIEDRDFLVRYACEPTAEKFVPIDIFQIIRRVKEMEPKQSDEYLKRVSV 213
                                     7        17         -        37        47        57        67        |-     |  87        97       107       117       127       137       147       157       167       177       187       197       207      
                                              17                  37                                     76     83

Legend:		→ Mismatch	(orange background)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: BAH domain (8)

Family: automated matches (5)

Protein domain: automated matches (5)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (2)

1a	d2fvua_	A:
1b	d2fvub_	B:

(no "CATH Domain" information available for 2FVU)

(no "Pfam Domain" information available for 2FVU)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SIR3_YEAST | P06701)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0031493	nucleosomal histone binding	Interacting selectively and non-covalently with a histone that is assembled into a nucleosome.
	GO:0031491	nucleosome binding	Interacting selectively and non-covalently with a nucleosome, a complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
biological process
	GO:0030466	chromatin silencing at silent mating-type cassette	Repression of transcription at silent mating-type loci by alteration of the structure of chromatin.
	GO:0031507	heterochromatin assembly	The assembly of chromatin into heterochromatin, a compact and highly condensed form that is often, but not always, transcriptionally silent.
	GO:0001308	negative regulation of chromatin silencing involved in replicative cell aging	The process, which occurs as a dividing cell ages, leading to expression of genes that are typically not expressed due to silencing by regulatory proteins.
	GO:0070481	nuclear-transcribed mRNA catabolic process, non-stop decay	The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that is lacking a stop codon.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005677	chromatin silencing complex	Any protein complex that mediates changes in chromatin structure that result in transcriptional silencing.
	GO:0000781	chromosome, telomeric region	The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0005720	nuclear heterochromatin	A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
	GO:0005724	nuclear telomeric heterochromatin	Heterochromatic regions of the chromosome found at the telomeres of a chromosome in the nucleus.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	2fvu
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	SIR3_YEAST \| P06701	:	2fl7 3owt 3te6 3tu4 3zco 4jjn 4kud 4kui 4kul 4ld9

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