DP00720: FACT complex subunit Ssrp1FASTA viewXML view

General information
DisProt:DP00720
Name:FACT complex subunit Ssrp1
Synonym(s):SSRP1_DROME
Chorion-factor 5
Facilitates chromatin transcription complex subunit Ssrp1
Recombination signal sequence recognition protein
Single-strand recognition protein
dSSRP1
First appeared in release:Release 5.9 (02/23/2012)
UniProt:Q05344
UniGene: 
SwissProt: SSRP1_DROME
TrEMBL:  
NCBI (GI):  
Source organism:Drosophila melanogaster (Fruit fly)
Sequence length:723
Percent disordered:100%
Homologues: 


Native sequence

        10         20         30         40         50         60
         |          |          |          |          |          |
MTDSLEYNDI NAEVRGVLCS GRLKMTEQNI IFKNTKTGKV EQISAEDIDL INSQKFVGTW - 60
GLRVFTKGGV LHRFTGFRDS EHEKLGKFIK AAYSQEMVEK EMCVKGWNWG TARFMGSVLS - 120
FDKESKTIFE VPLSHVSQCV TGKNEVTLEF HQNDDAPVGL LEMRFHIPAV ESAEEDPVDK - 180
FHQNVMSKAS VISASGESIA IFREIQILTP RGRYDIKIFS TFFQLHGKTF DYKIPMDSVL - 240
RLFMLPHKDS RQMFFVLSLD PPIKQGQTRY HYLVLLFAPD EETTIELPFS EAELRDKYEG - 300
KLEKEISGPV YEVMGKVMKV LIGRKITGPG NFIGHSGTAA VGCSFKAAAG YLYPLERGFI - 360
YIHKPPLHIR FEEISSVNFA RSGGSTRSFD FEVTLKNGTV HIFSSIEKEE YAKLFDYITQ - 420
KKLHVSNMGK DKSGYKDVDF GDSDNENEPD AYLARLKAEA REKEEDDDDG DSDEESTDED - 480
FKPNENESDV AEEYDSNVES DSDDDSDASG GGGDSDGAKK KKEKKSEKKE KKEKKHKEKE - 540
RTKKPSKKKK DSGKPKRATT AFMLWLNDTR ESIKRENPGI KVTEIAKKGG EMWKELKDKS - 600
KWEDAAAKDK QRYHDEMRNY KPEAGGDSDN EKGGKSSKKR KTEPSPSKKA NTSGSGFKSK - 660
EYISDDDSTS SDDEKDNEPA KKKSKPPSDG DAKKKKAKSE SEPEESEEDS NASDEDEEDE - 720
ASD



Functional narrative    

Function: Component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair. During transcription elongation the FACT complex acts as a histone chaperone that both destabilizes and restores nucleosomal structure. It facilitates the passage of RNA polymerase II and transcription by promoting the dissociation of one histone H2A-H2B dimer from the nucleosome, then subsequently promotes the reestablishment of the nucleosome following the passage of RNA polymerase II. Binds specifically to single-stranded DNA and RNA with highest affinity for nucleotides G and U. The FACT complex is required for expression of Hox genes.
SUBUNIT: Component of the FACT complex, a stable heterodimer of dre4/spt16 and Ssrp. Interacts with CHD1 and TRL/GAGA.


Subcellular Location: Nucleus. Chromosome. Note=Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci.
TISSUE SPECIFICITY: Expressed at highest levels in nurse cells of the ovary.
DEVELOPMENTAL STAGE: Abundant throughout oogenesis and embryogenesis, decreases during larval stages and increases again in pupae.
SIMILARITY: Belongs to the SSRP1 family.
SIMILARITY: Contains 1 HMG box DNA-binding domain.
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Region 1: 1-433 Region 2: 434-518 Region 3: 519-554 Region 4: 555-624 Region 5: 625-723

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:Disordered
Name:N-terminal domain
Location:1 - 433
Length:433
Region sequence:

MTDSLEYNDINAEVRGVLCSGRLKMTEQNIIFKNTKTGKVEQISAEDIDLINSQKFVGTW
GLRVFTKGGVLHRFTGFRDSEHEKLGKFIKAAYSQEMVEKEMCVKGWNWGTARFMGSVLS
FDKESKTIFEVPLSHVSQCVTGKNEVTLEFHQNDDAPVGLLEMRFHIPAVESAEEDPVDK
FHQNVMSKASVISASGESIAIFREIQILTPRGRYDIKIFSTFFQLHGKTFDYKIPMDSVL
RLFMLPHKDSRQMFFVLSLDPPIKQGQTRYHYLVLLFAPDEETTIELPFSEAELRDKYEG
KLEKEISGPVYEVMGKVMKVLIGRKITGPGNFIGHSGTAAVGCSFKAAAGYLYPLERGFI
YIHKPPLHIRFEEISSVNFARSGGSTRSFDFEVTLKNGTVHIFSSIEKEEYAKLFDYITQ
KKLHVSNMGKDKS

Modification type: Native
PDB:  
Structural/functional type:  
Functional classes: Molecular recognition effectors
Functional subclasses: Protein-DNA binding
Detection methods:
  1. Atomic force microscopy (AFM) (pH: 7.5; FACT complex (FACT subunits SSRP1 and SPT16 in Buffer A) 2 uL; Buffer A (Tris-HCl, NaCl, glycerol, ME); Tris-HCl (Buffer B for AFM observation) 20 mM; MgCl2 (Buffer B for AFM observation) 10 mM; KCl (Buffer B for AFM observation) 50 mM)
References:
  1. Miyagi A, Tsunaka Y, Uchihashi T, Mayanagi K, Hirose S, Morikawa K, Ando T. "Visualization of intrinsically disordered regions of proteins by high-speed atomic force microscopy." Chemphyschem. 2008; 9(13): 1859-66. PubMed: 18698566

  2. Tsunaka Y, Toga J, Yamaguchi H, Tate S, Hirose S, Morikawa K. "Phosphorylated intrinsically disordered region of FACT masks its nucleosomal DNA binding elements." J. Biol. Chem.. 2009; 284(36): 24610-21. PubMed: 19605348
Comments:
The N-terminal domain contains a structure-specific recognition (SSRC) motif at aa M186-K436.


Region 2
Type:Disordered - Extended
Name:IDR-Acidic
Location:434 - 518
Length:85
Region sequence:

GYKDVDFGDSDNENEPDAYLARLKAEAREKEEDDDDGDSDEESTDEDFKPNENESDVAEE
YDSNVESDSDDDSDASGGGGDSDGA

Modification type: Complex
Native
PDB:  
Structural/functional type: Function arises from the disordered state
Functional classes: Modification site
Molecular recognition effectors
Functional subclasses: Intraprotein interaction
Phosphorylation
Protein-protein binding
Detection methods:
  1. Atomic force microscopy (AFM) (pH: 7.5; Buffer A (Tris-HCl, NaCl, glycerol, ME); FACT complex (FACT subunits SSRP1 and SPT16 in Buffer A) 2 uL; KCl (Buffer B for AFM observation) 50 mM; MgCl2 (Buffer B for AFM observation) 10 mM; Tris-HCl (Buffer B for AFM observation) 20 mM)

  2. Circular dichroism (CD) spectroscopy, far-UV (298 K; pH: 8.5; 2-mercaptoethanol 5 mM; dSSRP1 protein (Sf9-Mid-dSSRP1 (aa 186-624) ); NaCl 0.15 M; Tris-HCL 20 mM)
References:
  1. Miyagi A, Tsunaka Y, Uchihashi T, Mayanagi K, Hirose S, Morikawa K, Ando T. "Visualization of intrinsically disordered regions of proteins by high-speed atomic force microscopy." Chemphyschem. 2008; 9(13): 1859-66. PubMed: 18698566

  2. Tsunaka Y, Toga J, Yamaguchi H, Tate S, Hirose S, Morikawa K. "Phosphorylated intrinsically disordered region of FACT masks its nucleosomal DNA binding elements." J. Biol. Chem.. 2009; 284(36): 24610-21. PubMed: 19605348
Comments:
Tsunaka et al (2009) describe that phosphorylation of the Acidic intrinsically disordered region (IDR) inhibits DNA binding of the HMG-box and Basic IDR regions.


Region 3
Type:Disordered - Extended
Name:IDR-Basic
Location:519 - 554
Length:36
Region sequence:

KKKKEKKSEKKEKKEKKHKEKERTKKPSKKKKDSGK

Modification type: Complex
Native
PDB:  
Structural/functional type: Function arises from the disordered state
Functional classes: Modification site
Molecular recognition effectors
Molecular assembly
Functional subclasses: Intraprotein interaction
Phosphorylation
Protein-DNA binding
Detection methods:
  1. Atomic force microscopy (AFM) (pH: 7.5; Buffer A (Tris-HCl, NaCl, glycerol, ME); FACT complex (FACT subunits SSRP1 and SPT16 in Buffer A) 2 uL; KCl (Buffer B for AFM observation) 50 mM; MgCl2 (Buffer B for AFM observation) 10 mM; Tris-HCl (Buffer B for AFM observation) 20 mM)

  2. Circular dichroism (CD) spectroscopy, far-UV (298 K; pH: 8.5; 2-mercaptoethanol 5 mM; dSSRP1 protein (Sf9-Mid-dSSRP1 (aa 186-624)); NaCl 0.15 M; Tris-HCL 20 mM)
References:
  1. Miyagi A, Tsunaka Y, Uchihashi T, Mayanagi K, Hirose S, Morikawa K, Ando T. "Visualization of intrinsically disordered regions of proteins by high-speed atomic force microscopy." Chemphyschem. 2008; 9(13): 1859-66. PubMed: 18698566

  2. Tsunaka Y, Toga J, Yamaguchi H, Tate S, Hirose S, Morikawa K. "Phosphorylated intrinsically disordered region of FACT masks its nucleosomal DNA binding elements." J. Biol. Chem.. 2009; 284(36): 24610-21. PubMed: 19605348
Comments:
Tsunaka et al (2009) describe that phosphorylation of the Acidic intrinsically disordered region (IDR) inhibits DNA binding of the HMG-box and Basic IDR regions.


Region 4
Type:Disordered
Name:HMG-box domain
Location:555 - 624
Length:70
Region sequence:

PKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSKWEDAAAKDKQRYH
DEMRNYKPEA

Modification type: Complex
Fragment
Native
PDB: 1WXL:A
Structural/functional type: Function arises from the disordered state
Functional classes: Molecular recognition effectors
Molecular assembly
Functional subclasses: Intraprotein interaction
Protein-DNA binding
Detection methods:
  1. Atomic force microscopy (AFM) (pH: 7.5; Buffer A (Tris-HCl, NaCl, glycerol, ME); FACT complex (FACT subunits SSRP1 and SPT16 in Buffer A) 2 uL; KCl (Buffer B for AFM observation) 50 mM; MgCl2 (Buffer B for AFM observation) 10 mM; Tris-HCl (Buffer B for AFM observation) 20 mM)

  2. Nuclear magnetic resonance (NMR) (298 K; pH: 5.2; dFACT HMG domain (protein fragment) 2.2 mM; H2O/D2O (90%/10%, solvent); sodium acetate (buffer) 2 mM)

  3. Circular dichroism (CD) spectroscopy, far-UV (298 K; pH: 8.5; 2-mercaptoethanol 5 mM; dSSRP1 protein (Sf9-Mid-dSSRP1 (aa 186-624)); NaCl 0.15 M; Tris-HCl 20 mM)
References:
  1. Kasai N, Tsunaka Y, Ohki I, Hirose S, Morikawa K, Tate S. "Solution structure of the HMG-box domain in the SSRP1 subunit of FACT." J. Biomol. NMR. 2005; 32(1): 83-8. PubMed: 16041486

  2. Miyagi A, Tsunaka Y, Uchihashi T, Mayanagi K, Hirose S, Morikawa K, Ando T. "Visualization of intrinsically disordered regions of proteins by high-speed atomic force microscopy." Chemphyschem. 2008; 9(13): 1859-66. PubMed: 18698566

  3. Tsunaka Y, Toga J, Yamaguchi H, Tate S, Hirose S, Morikawa K. "Phosphorylated intrinsically disordered region of FACT masks its nucleosomal DNA binding elements." J. Biol. Chem.. 2009; 284(36): 24610-21. PubMed: 19605348
Comments:
PDB structure 1WXL, from Kasai et al (2005), was characterized using protein fragment comprising the HMG-box domain, aa P555-A624.

Secondary structure of HMG-box domain consists of three alpha-helices at A561-R575, V582-K594 and S600-R618 connected by loops at E576-K581 and E595-K599.

Tsunaka et al (2009) describe that phosphorylation of the Acidic intrinsically disordered region (IDR) inhibits DNA binding of the HMG-box and Basic IDR regions.


Region 5
Type:Disordered - Extended
Name:IDR-Mixed
Location:625 - 723
Length:99
Region sequence:

GGDSDNEKGGKSSKKRKTEPSPSKKANTSGSGFKSKEYISDDDSTSSDDEKDNEPAKKKS
KPPSDGDAKKKKAKSESEPEESEEDSNASDEDEEDEASD

Modification type: Native
PDB:  
Structural/functional type: Function arises from the disordered state
Functional classes: Modification site
Molecular recognition effectors
Functional subclasses: Intraprotein interaction
Phosphorylation
Detection methods:
  1. Atomic force microscopy (AFM) (pH: 7.5; Buffer A (Tris-HCl, NaCl, glycerol, ME); FACT complex (FACT subunits SSRP1 and SPT16 in Buffer A) 2 uL; KCl (Buffer B for AFM observation) 50 mM; MgCl2 (Buffer B for AFM observation) 10 mM; Tris-HCl (Buffer B for AFM observation) 20 mM)
References:
  1. Miyagi A, Tsunaka Y, Uchihashi T, Mayanagi K, Hirose S, Morikawa K, Ando T. "Visualization of intrinsically disordered regions of proteins by high-speed atomic force microscopy." Chemphyschem. 2008; 9(13): 1859-66. PubMed: 18698566

  2. Tsunaka Y, Toga J, Yamaguchi H, Tate S, Hirose S, Morikawa K. "Phosphorylated intrinsically disordered region of FACT masks its nucleosomal DNA binding elements." J. Biol. Chem.. 2009; 284(36): 24610-21. PubMed: 19605348
Comments:
The IDR-Mixed region consists of interspersed basic and acidic segments. It also contains phosphorylation sites, but these were not involved in the DNA-binding inhibitory effect found with the Acidic IDR (Tsunaka 2009).


References

  1. Fuxreiter M, Simon I, Bondos S. "Dynamic protein-DNA recognition: beyond what can be seen." Trends Biochem. Sci.. 2011; 36(8): 415-23. PubMed: 21620710



Comments


A discussion of the dynamic nature and competitive binding of FACT in a "fuzzy" protein-DNA complex is found in Fuxreiter et al (2011).


Verification request sent 2-22-2012 (PMID: 18698566)


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