DP00533: Regulatory protein SIR3FASTA viewXML view

General information
DisProt:DP00533
Name:Regulatory protein SIR3
Synonym(s):SIR3_YEAST
Silent information regulator 3
First appeared in release:Release 6.00 (07/01/2012)
UniProt:P06701
UniGene: 
SwissProt: SIR3_YEAST
TrEMBL:  
NCBI (GI): 1711392
Source organism:Saccharomyces cerevisiae (Baker's yeast)
Sequence length:978
Percent disordered:34%
Homologues: 


Native sequence

        10         20         30         40         50         60
         |          |          |          |          |          |
MAKTLKDLDG WQVIITDDQG RVIDDNNRRR SRKRGGENVF LKRISDGLSF GKGESVIFND - 60
NVTETYSVYL IHEIRLNTLN NVVEIWVFSY LRWFELKPKL YYEQFRPDLI KEDHPLEFYK - 120
DKFFNEVNKS ELYLTAELSE IWLKDFIAVG QILPESQWND SSIDKIEDRD FLVRYACEPT - 180
AEKFVPIDIF QIIRRVKEME PKQSDEYLKR VSVPVSGQKT NRQVMHKMGV ERSSKRLAKK - 240
PSMKKIKIEP SADDDVNNGN IPSQRGTSTT HGSISPQEES VSPNISSASP SALTSPTDSS - 300
KILQKRSISK ELIVSEEIPI NSSEQESDYE PNNETSVLSS KPGSKPEKTS TELVDGRENF - 360
VYANNPEVSD DGGLEEETDE VSSESSDEAI IPVNKRRGAH GSELSSKIRK IHIQETQEFS - 420
KNYTTETDNE MNGNGKPGIP RGNTKIHSMN ENPTPEKGNA KMIDFATLSK LKKKYQIILD - 480
RFAPDNQVTD SSQLNKLTDE QSSLDVAGLE DKFRKACSSS GRETILSNFN ADINLEESIR - 540
ESLQKRELLK SQVEDFTRIF LPIYDSLMSS QNKLFYITNA DDSTKFQLVN DVMDELITSS - 600
ARKELPIFDY IHIDALELAG MDALYEKIWF AISKENLCGD ISLEALNFYI TNVPKAKKRK - 660
TLILIQNPEN LLSEKILQYF EKWISSKNSK LSIICVGGHN VTIREQINIM PSLKAHFTEI - 720
KLNKVDKNEL QQMIITRLKS LLKPFHVKVN DKKEMTIYNN IREGQNQKIP DNVIVINHKI - 780
NNKITQLIAK NVANVSGSTE KAFKICEAAV EISKKDFVRK GGLQKGKLVV SQEMVPRYFS - 840
EAINGFKDET ISKKIIGMSL LMRTFLYTLA QETEGTNRHT LALETVLIKM VKMLRDNPGY - 900
KASKEIKKVI CGAWEPAITI EKLKQFSWIS VVNDLVGEKL VVVVLEEPSA SIMVELKLPL - 960
EINYAFSMDE EFKNMDCI



Functional narrative    

The silent information regulator protein 3 (Sir3p) functions in the initiation, propagation, and maintenance of transcriptionally silenced chromatin in Saccharomyces cerevisiae. The Sir3p monomer has a unique tripartite domain organization, including a stretch of nearly 300 residues that are intrinsically disordered, which lie internal to the structured N- and C-terminal regions. The proteins SIR1 through SIR4 are required for transcriptional repression of the silent mating type loci, HML and HMR. The proteins SIR2 through SIR4 repress mulitple loci by modulating chromatin structure. Involves the compaction of chromatin fiber into a more condensed form.

Region 1: 1-215 Region 2: 216-550 Region 3: 551-978

Map of ordered and disordered regions







Note: 'Mouse' over a region to see the start and stop residues. Click on a region to see detailed information.


Region 1
Type:Ordered
Name:N-terminal region
Location:1 - 215
Length:215
Region sequence:

MAKTLKDLDGWQVIITDDQGRVIDDNNRRRSRKRGGENVFLKRISDGLSFGKGESVIFND
NVTETYSVYLIHEIRLNTLNNVVEIWVFSYLRWFELKPKLYYEQFRPDLIKEDHPLEFYK
DKFFNEVNKSELYLTAELSEIWLKDFIAVGQILPESQWNDSSIDKIEDRDFLVRYACEPT
AEKFVPIDIFQIIRRVKEMEPKQSDEYLKRVSVPV

Modification type: Engineered
Fragment
Native
PDB: 2FL7:A, 2FVU:A, 3TU4:K
Structural/functional type: Function arises from the ordered state
Functional classes: Molecular assembly
Functional subclasses: Intraprotein interaction
Protein-DNA binding
Protein-protein binding
Detection methods:
  1. Circular dichroism (CD) spectroscopy, far-UV (293 K; Sir3p 1 uM; NaCl 0.5 M; GuHCl)

  2. Sensitivity to proteolysis (Trypsin)

  3. Analytical ultracentrifugation (294 K; )

  4. X-ray crystallography (298 K; pH: 6.5; 1) NTD of Sir3p (aa 1-229) (PDB 2FL7); HEPES 0.1 M; NaCl 200 mM; PEG400 (10%))

  5. X-ray crystallography (290 K; pH: 3.75; 1) NTD of Sir3p (aa 1-218) (PDB 2FVU); sodium formate 4 M)

  6. X-ray crystallography (294 K; pH: 7; 1) NTD of Sir3p (aa 1-213) (PDB 3TU4); nucleosome core particle (NCP) (in complex))

References:
  1. Armache KJ, Garlick JD, Canzio D, Narlikar GJ, Kingston RE. "Structural basis of silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 Å resolution." Science. 2011; 334(6058): 977-82. PubMed: 22096199

  2. Connelly JJ, Yuan P, Hsu HC, Li Z, Xu RM, Sternglanz R. "Structure and function of the Saccharomyces cerevisiae Sir3 BAH domain." Mol. Cell. Biol.. 2006; 26(8): 3256-65. PubMed: 16581798

  3. Hou Z, Danzer JR, Fox CA, Keck JL. "Structure of the Sir3 protein bromo adjacent homology (BAH) domain from S. cerevisiae at 1.95 A resolution." Protein Sci.. 2006; 15(5): 1182-6. PubMed: 16641491

  4. McBryant SJ, Krause C, Hansen JC. "Domain Organization and Quaternary Structure of the Saccharomyces cerevisiae Silent Information Regulator 3 Protein, Sir3p." Biochemistry. 2006; 45(51): 15941-8. PubMed: 17176117

Comments:
N-terminal region contains the bromo adjacent homology (BAH) domain at ~aa L48-D188.

Experiments by McBryant et al (2006), (CD, proteolysis, analytical centrifugation) were performed using recombinant Sir3p.

PDB 2FL7 is from Hou et al (2006), PDB 2FVU is from Connelly et al (2006), PDB 3TU4 is in complex with NCP and is from Armache et al (2011).




Region 2
Type:Disordered
Name:central disordered region
Location:216 - 550
Length:335
Region sequence:

SGQKTNRQVMHKMGVERSSKRLAKKPSMKKIKIEPSADDDVNNGNIPSQRGTSTTHGSIS
PQEESVSPNISSASPSALTSPTDSSKILQKRSISKELIVSEEIPINSSEQESDYEPNNET
SVLSSKPGSKPEKTSTELVDGRENFVYANNPEVSDDGGLEEETDEVSSESSDEAIIPVNK
RRGAHGSELSSKIRKIHIQETQEFSKNYTTETDNEMNGNGKPGIPRGNTKIHSMNENPTP
EKGNAKMIDFATLSKLKKKYQIILDRFAPDNQVTDSSQLNKLTDEQSSLDVAGLEDKFRK
ACSSSGRETILSNFNADINLEESIRESLQKRELLK

Modification type: Engineered
Native
PDB: 3OWT:C
Structural/functional type: Function arises from the disordered state
Functional classes: Molecular assembly
Functional subclasses: Intraprotein interaction
Protein-DNA binding
Protein-protein binding
Detection methods:
  1. Circular dichroism (CD) spectroscopy, far-UV (293 K; GuHCl; NaCl 0.5 M; Sir3p 1 uM)

  2. Sensitivity to proteolysis (Trypsin)

  3. Analytical ultracentrifugation (294 K; )

  4. X-ray crystallography (277 K; pH: 4.8; 1) Sir3p fragment (aa 456-481) (PDB 3OWT); ammonium acetate 200 mM; DTT 10 mm; PEG4K (30%); RAP1 fragment (aa 672-827) (in complex); sodium citrate 100 mM)

References:
  1. Chen Y, Rai R, Zhou ZR, Kanoh J, Ribeyre C, Yang Y, Zheng H, Damay P, Wang F, Tsujii H, Hiraoka Y, Shore D, Hu HY, Chang S, Lei M. "A conserved motif within RAP1 has diversified roles in telomere protection and regulation in different organisms." Nat. Struct. Mol. Biol.. 2011; 18(2): 213-21. PubMed: 21217703

  2. McBryant SJ, Krause C, Hansen JC. "Domain Organization and Quaternary Structure of the Saccharomyces cerevisiae Silent Information Regulator 3 Protein, Sir3p." Biochemistry. 2006; 45(51): 15941-8. PubMed: 17176117

Comments:
Experiments by McBryant et al (2006), (CD, proteolysis, analytical centrifugation) were performed using recombinant Sir3p.

According to McBryant et al (2006), the central region is "largely disordered, including two long stretches (residues 220-275 and 325-475) that are predicted to almost completely lack order." Additionally, they note this central region contains "islands of order."

PDB structure 3OWT, chain C, from Chen et al (2011), contains a small fragment of the central region comprising the RAP1-interaction motif (E456-R481) in complex with DNA-binding protein RAP1.




Region 3
Type:Ordered
Name:C-terminal region
Location:551 - 978
Length:428
Region sequence:

SQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDY
IHIDALELAGMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPEN
LLSEKILQYFEKWISSKNSKLSIICVGGHNVTIREQINIMPSLKAHFTEIKLNKVDKNEL
QQMIITRLKSLLKPFHVKVNDKKEMTIYNNIREGQNQKIPDNVIVINHKINNKITQLIAK
NVANVSGSTEKAFKICEAAVEISKKDFVRKGGLQKGKLVVSQEMVPRYFSEAINGFKDET
ISKKIIGMSLLMRTFLYTLAQETEGTNRHTLALETVLIKMVKMLRDNPGYKASKEIKKVI
CGAWEPAITIEKLKQFSWISVVNDLVGEKLVVVVLEEPSASIMVELKLPLEINYAFSMDE
EFKNMDCI

Modification type: Engineered
Native
PDB: 3TE6:A
Structural/functional type: Function arises from the ordered state
Functional classes: Molecular assembly
Functional subclasses: Intraprotein interaction
Protein-DNA binding
Protein-protein binding
Detection methods:
  1. Circular dichroism (CD) spectroscopy, far-UV (293 K; GuHCl; NaCl 0.5 M; Sir3p 1 uM)

  2. Sensitivity to proteolysis (Trypsin)

  3. Analytical ultracentrifugation (294 K; )

  4. X-ray crystallography (277 K; pH: 7.5; 1) Sir3p fragment (aa 530-845) (PDB 3TE6); ammonium sulfate 2 M; HEPES 0.1 M; PEG 400 (2% (w/v)))

References:
  1. Ehrentraut S, Hassler M, Oppikofer M, Kueng S, Weber JM, Mueller JW, Gasser SM, Ladurner AG, Ehrenhofer-Murray AE. "Structural basis for the role of the Sir3 AAA+ domain in silencing: interaction with Sir4 and unmethylated histone H3K79." Genes Dev.. 2011; 25(17): 1835-46. PubMed: 21896656

  2. McBryant SJ, Krause C, Hansen JC. "Domain Organization and Quaternary Structure of the Saccharomyces cerevisiae Silent Information Regulator 3 Protein, Sir3p." Biochemistry. 2006; 45(51): 15941-8. PubMed: 17176117

Comments:
Experiments by McBryant et al (2006), (CD, proteolysis, analytical centrifugation) were performed using recombinant Sir3p.

PDB structure 3TE6, from Ehrentraut et al (2011), shows the AAA+ ATPase-like domain (N530-G845).




References

  1. Adkins NL, McBryant SJ, Johnson CN, Leidy JM, Woodcock CL, Robert CH, Hansen JC, Georgel PT. "Role of nucleic acid binding in Sir3p-dependent interactions with chromatin fibers." Biochemistry. 2009; 48(2): 276-88. PubMed: 19099415

  2. McBryant SJ, Krause C, Hansen JC. "Domain Organization and Quaternary Structure of the Saccharomyces cerevisiae Silent Information Regulator 3 Protein, Sir3p." Biochemistry. 2006; 45(51): 15941-8. PubMed: 17176117

  3. McBryant SJ, Krause C, Woodcock CL, Hansen JC. "The silent information regulator 3 protein, SIR3p, binds to chromatin fibers and assembles a hypercondensed chromatin architecture in the presence of salt." Mol. Cell. Biol.. 2008; 28(11): 3563-72. PubMed: 18362167



Comments


Regions 1-3 are delineated by McBryant et al (2006). Additional discussion of Sir3p-chromatin interactions is found in McBryant et al (2008) and Adkins et al (2009).



AV sent 6/19/2012 (PMID:17176117)


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