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(-) Description

Title :  CRYSTAL STRUCTURE OF THE S. CEREVISIAE SIR3 AAA+ DOMAIN
 
Authors :  M. Hassler, A. G. Ladurner
Date :  12 Aug 11  (Deposition) - 31 Aug 11  (Release) - 14 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Heterochromatin, Gene Silencing, Sir Complex, Hmr, Hml, Telomere, Aaa+ Domain, Structural, Sir4, Sir3, Sir2, Nucleus, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ehrentraut, M. Hassler, M. Oppikofer, S. Kueng, J. M. Weber, J. W. Mueller, S. M. Gasser, A. G. Ladurner, A. E. Ehrenhofer-Murray
Structural Basis For The Role Of The Sir3 Aaa+ Domain In Silencing: Interaction With Sir4 And Unmethylated Histone H3K79.
Genes Dev. V. 25 1835 2011
PubMed-ID: 21896656  |  Reference-DOI: 10.1101/GAD.17175111

(-) Compounds

Molecule 1 - REGULATORY PROTEIN SIR3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET41
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: AAA+ DOMAIN (UNP RESIDUES 530-845)
    Gene: SIR3, CMT1, MAR2, STE8, YLR442C, L9753.10
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: SILENT INFORMATION REGULATOR 3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3TE6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TE6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:529 -Asn A:530

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TE6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TE6)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR442C1YLR442C.1XII:1022248-10193122937SIR3_YEAST1-9789782A:529-844 (gaps)
B:529-844 (gaps)		316
316

(-) Sequences/Alignments

Asymmetric 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:304
 aligned with SIR3_YEAST | P06701 from UniProtKB/Swiss-Prot  Length:978

    Alignment length:316
                                   538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838      
           SIR3_YEAST   529 FNADINLEESIRESLQKRELLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLLSEKILQYFEKWISSKNSKLSIICVGGHNVTIREQINIMPSLKAHFTEIKLNKVDKNELQQMIITRLKSLLKPFHVKVNDKKEMTIYNNIREGQNQKIPDNVIVINHKINNKITQLIAKNVANVSGSTEKAFKICEAAVEISKKDFVRKGGLQKGKLVVSQEMVPRYFSEAIN 844
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhh........eeeeeee....--.hhhhhhhhhhhh...--...hhhhhhhhhhhhhhhhh.eeeeeee.......hhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh..eeeee.....eee...--------....eeee.ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee..ee...ee..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:529-844 (gaps) UniProt: 1-978 [INCOMPLETE]                                                                                                                                                                                                                                                                  Transcript 1
                 3te6 A 529 PNADINLEESIRESLQKRELLKSQVEDFTRIFLPIYDSLmSSQNKLFYITNADDSTKFQLVNDVmDELITSSARKELPIFDYIHIDALEL--mDALYEKIWFAISKEN--GDISLEALNFYITNVPKAKKRKTLILIQNPENLLSEKILQYFEKWISSKNSKLSIICVGGHNVTIREQINImPSLKAHFTEIKLNKVDKNELQQmIITRLKSLLKPFHVKVNDKKEmTIYNN--------IPDNVIVINHKINNKITQLIAKNVANVSGSTEKAFKICEAAVEISKKDFVRKGGLQKGKLVVSQEmVPRYFSEAIN 844
                                   538       548       558       568       578       588    |  598       608       618  |    628       | -|      648       658       668       678       688       698       708 |     718       728    |  738       748      |758 |       -|      778       788       798       808       818       828     | 838      
                                                                 568-MSE                  593-MSE                  618  |            636  |                                                                    710-MSE                733-MSE               755-MSE0      769                                                              834-MSE      
                                                                                                                      621-MSE           639                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:303
 aligned with SIR3_YEAST | P06701 from UniProtKB/Swiss-Prot  Length:978

    Alignment length:316
                                   538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838      
           SIR3_YEAST   529 FNADINLEESIRESLQKRELLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLLSEKILQYFEKWISSKNSKLSIICVGGHNVTIREQINIMPSLKAHFTEIKLNKVDKNELQQMIITRLKSLLKPFHVKVNDKKEMTIYNNIREGQNQKIPDNVIVINHKINNKITQLIAKNVANVSGSTEKAFKICEAAVEISKKDFVRKGGLQKGKLVVSQEMVPRYFSEAIN 844
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhh......eeeeee...---.hhhhhhhhhh...--..hhhhhhhhhhhhhh.hhhhh..eeeeee......hhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhheeeee....hhhhhhhhhhhhhhhhh...eeee.....eeee..--------....eee.eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee..ee..eee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:529-844 (gaps) UniProt: 1-978 [INCOMPLETE]                                                                                                                                                                                                                                                                  Transcript 1
                 3te6 B 529 PNADINLEESIRESLQKRELLKSQVEDFTRIFLPIYDSLmSSQNKLFYITNADDSTKFQLVNDVmDELITSSARKELPIFDYIHIDALE---mDALYEKIWFAISK--LCGDISLEALNFYITNVPKAKKRKTLILIQNPENLLSEKILQYFEKWISSKNSKLSIICVGGHNVTIREQINImPSLKAHFTEIKLNKVDKNELQQmIITRLKSLLKPFHVKVNDKKEmTIYNN--------IPDNVIVINHKINNKITQLIAKNVANVSGSTEKAFKICEAAVEISKKDFVRKGGLQKGKLVVSQEmVPRYFSEAIN 844
                                   538       548       558       568       578       588    |  598       608        |-  |    628     | 638       648       658       668       678       688       698       708 |     718       728    |  738       748      |758 |       -|      778       788       798       808       818       828     | 838      
                                                                 568-MSE                  593-MSE                 617   |          634  |                                                                      710-MSE                733-MSE               755-MSE0      769                                                              834-MSE      
                                                                                                                      621-MSE         637
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3TE6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TE6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TE6)

(-) Gene Ontology  (21, 21)

Asymmetric 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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SIR3_YEAST | P06701: 2fl7 2fvu 3owt 3tu4 3zco 4jjn 4kud 4kui 4kul 4ld9

(-) Related Entries Specified in the PDB File

1nyh CRYSTAL STRUCTURE OF THE COILED-COIL DIMERIZATION MOTIF OF SIR4
2fl7 S. CEREVISIAE SIR3 BAH DOMAIN
2fvu STRUCTURE OF THE YEAST SIR3 BAH DOMAIN
3owt CRYSTAL STRUCTURE OF S. CEREVISIAE RAP1-SIR3 COMPLEX