Heliks-zavoj-heliks

λ represor bakteriofaga lambda koristi heliks-zavoj-heliks (levo; zeleno) da se veže za DNK (desno; plavo i crveno).

U proteinima, heliks-zavoj-heliks (HTH) je glavni strukturni motiv sa sposobnošću vezivanja za DNK. On se sastoji od dva α heliksa spojena kratkim lancom aminokiselina. Prisutan je u mnogim proteinima koji regulišu ekspresiju gena. On se razlikuje od domena heliks-petlja-heliks.[1]

Otkriće

Otkriće heliks-zavoj-heliks motiva je bilo bazirano na sličnostima između nekoliko gena koji koriraju transkripcione regulatorne proteine iz bakteriofaga lambda i Escherichia coli: Cro, CAP, i λ represor, za koje je najđeno da imaju zajedničku 20-25 aminokiselina dugu sekvencu koja omogućava DNK prepoznavanje.[2][3][4][5]

Reference

  1. ↑ Brennan RG, Matthews BW (1989). „The helix-turn-helix DNA binding motif.”. J Biol Chem 264 (4): 1903–6. PMID 2644244. 
  2. ↑ Matthews BW, Ohlendorf DH, Anderson WF, Takeda Y (1982). „Structure of the DNA-binding region of lac repressor inferred from its homology with cro repressor.”. Proc Natl Acad Sci U S A 79 (5): 1428–32. PMC 345986. PMID 6951187. 
  3. ↑ Anderson WF, Ohlendorf DH, Takeda Y, Matthews BW (1981). „Structure of the cro repressor from bacteriophage lambda and its interaction with DNA.”. Nature 290 (5809): 754–8. PMID 6452580. 
  4. ↑ McKay DB, Steitz TA (1981). „Structure of catabolite gene activator protein at 2.9 A resolution suggests binding to left-handed B-DNA.”. Nature 290 (5809): 744–9. PMID 6261152. 
  5. ↑ Pabo CO, Lewis M (1982). „The operator-binding domain of lambda repressor: structure and DNA recognition.”. Nature 298 (5873): 443–7. PMID 7088190. 

Literatura

  • Struhl K (1989). „Helix-turn-helix, zinc-finger, and leucine-zipper motifs for eukaryotic transcriptional regulatory proteins.”. Trends Biochem Sci 14 (4): 137–40. PMID 2499084. 
  • Gajiwala KS, Burley SK (2000). „Winged helix proteins.”. Curr Opin Struct Biol 10 (1): 110–6. PMID 10679470. 
  • Santos CL, Tavares F, Thioulouse J, Normand P (2009). „A phylogenomic analysis of bacterial helix-turn-helix transcription factors.”. FEMS Microbiol Rev 33 (2): 411–29. DOI:10.1111/j.1574-6976.2008.00154.x. PMID 19076237. 
  • Hoskisson PA, Rigali S (2009). „Chapter 1: Variation in form and function the helix-turn-helix regulators of the GntR superfamily.”. Adv Appl Microbiol 69: 1–22. DOI:10.1016/S0065-2164(09)69001-8. PMID 19729089. 
  • Brennan RG (1993). „The winged-helix DNA-binding motif: another helix-turn-helix takeoff.”. Cell 74 (5): 773–6. PMID 8374950. 
  • Huffman JL, Brennan RG (2002). „Prokaryotic transcription regulators: more than just the helix-turn-helix motif.”. Curr Opin Struct Biol 12 (1): 98–106. PMID 11839496. 

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Spoljašnje veze

  • Heliks-zavoj-heliks
  • PDB 1LMB Arhivirano 2004-10-29 na Wayback Machine-u
  • Cro/C1-type HTH domen
Heliks-zavoj-heliks domeni
Bakterijski regulatorni heliks-zavoj-heliks protein, lysR familija
Identifikatori
Simbol HTH_1
Pfam PF00126
Pfam klan CL0123
InterPro IPR000847
PROSITE PDOC00043
SCOP 1al3
Superfamilija 1al3
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
HTH DNA vezujući domen
Identifikatori
Simbol HTH_10
Pfam PF04967
Pfam klan CL0123
InterPro IPR007050
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Ribonukleazni R heliksni domen
Identifikatori
Simbol HTH_12
Pfam PF08461
Pfam klan CL0123
InterPro IPR013668
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
HTH DNA vezujući domen
Identifikatori
Simbol HTH_13
Pfam PF11972
Pfam klan CL0123
InterPro IPR021068
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Heliks-zavoj-heliks
Identifikatori
Simbol HTH_3
Pfam PF01381
Pfam klan CL0123
InterPro IPR001387
SCOP 1r69
Superfamilija 1r69
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Bakterijski regulatorni protein, arsR familija
Identifikatori
Simbol HTH_5
Pfam PF01022
Pfam klan CL0123
InterPro IPR001845
PROSITE PDOC00661
SCOP 1smt
Superfamilija 1smt
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Heliks-zavoj-heliks domen, rpiR familija
Identifikatori
Simbol HTH_6
Pfam PF01418
Pfam klan CL0123
InterPro IPR000281
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Heliks-zavoj-heliks domen rezolvaze
Identifikatori
Simbol HTH_7
Pfam PF02796
Pfam klan CL0123
InterPro IPR006120
PROSITE PDOC00334
SCOP 1hcr
Superfamilija 1hcr
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Bakterijski regulatorni protein, Fis familija
Identifikatori
Simbol HTH_8
Pfam PF02954
Pfam klan CL0123
InterPro IPR002197
SCOP 1f36
Superfamilija 1f36
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
RNA polimeraza III podjedinica RPC82 heliks-zavoj-heliks domen
Identifikatori
Simbol HTH_9
Pfam PF08221
Pfam klan CL0123
InterPro IPR013197
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Bakterijski regulatorni heliks-zavoj-heliks proteini, AraC familija
Identifikatori
Simbol HTH_AraC
Pfam PF00165
Pfam klan CL0123
InterPro IPR000005
PROSITE PDOC00040
SCOP 1bl0
Superfamilija 1bl0
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
CodY heliks-zavoj-heliks domen
Identifikatori
Simbol HTH_CodY
Pfam PF08222
Pfam klan CL0123
InterPro IPR013198
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
DeoR sličan heliks-zavoj-heliks domen
Identifikatori
Simbol HTH_DeoR
Pfam PF08220
Pfam klan CL0123
InterPro IPR001034
PROSITE PDOC00696
SCOP 1lk5
Superfamilija 1lk5
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
IclR heliks-zavoj-heliks domen
Identifikatori
Simbol HTH_IclR
Pfam PF09339
Pfam klan CL0123
InterPro IPR005471
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
M protein trans delujući pozitivni regulator (MGA) HTH domen
Identifikatori
Simbol HTH_Mga
Pfam PF08280
Pfam klan CL0123
InterPro IPR013199
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Heliks-zavoj-heliks domen
Identifikatori
Simbol HTH_OrfB_IS605
Pfam PF12323
Pfam klan CL0123
InterPro IPR021027
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Heliks-zavoj-heliks Psq domen
Identifikatori
Simbol HTH_psq
Pfam PF05225
Pfam klan CL0123
InterPro IPR007889
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Transposaza
Identifikatori
Simbol HTH_Tnp_1
Pfam PF01527
Pfam klan CL0123
InterPro IPR002514
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Transposaza
Identifikatori
Simbol HTH_Tnp_IS630
Pfam PF01710
Pfam klan CL0123
InterPro IPR002622
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Mi DNK vezujući domen
Identifikatori
Simbol HTH_Tnp_Mu_1
Pfam PF02316
Pfam klan CL0123
InterPro IPR003314
SCOP 1qpm
Superfamilija 1qpm
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Mi DNK Vezujući, I gama poddomen
Identifikatori
Simbol HTH_Tnp_Mu_2
Pfam PF09039
Pfam klan CL0123
InterPro IPR015126
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Transposaza
Identifikatori
Simbol HTH_Tnp_Tc3_2
Pfam PF01498
Pfam klan CL0123
InterPro IPR002492
SCOP 1tc3
Superfamilija 1tc3
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Tc5 transposaza DNA vezujući domen
Identifikatori
Simbol HTH_Tnp_Tc5
Pfam PF03221
Pfam klan CL0123
InterPro IPR004906
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Regulator sporulacije, WhiA C terminusni domen
Identifikatori
Simbol HTH_WhiA
Pfam PF02650
Pfam klan CL0123
InterPro IPR003802
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Heliks-zavoj-heliks domen alkil merkuri liaze
Identifikatori
Simbol HTH_15
Pfam PF12324
Pfam klan CL0123
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Heliks-zavoj-heliks domen
Identifikatori
Simbol HTH_16
Pfam PF12645
Pfam klan CL0123
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Heliks-zavoj-heliks domen
Identifikatori
Simbol HTH_17
Pfam PF12728
Pfam klan CL0123
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Heliks-zavoj-heliks domen
Identifikatori
Simbol HTH_18
Pfam PF12833
Pfam klan CL0123
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Heliks-zavoj-heliks domen
Identifikatori
Simbol HTH_19
Pfam PF12844
Pfam klan CL0123
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Heliks-zavoj-heliks domen
Identifikatori
Simbol HTH_20
Pfam PF12840
Pfam klan CL0123
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
InsA C-terminusni domen
Identifikatori
Simbol HTH_Tnp_IS1
Pfam PF12759
Pfam klan CL0123
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Heliks-zavoj-heliks domen transposaze IS66
Identifikatori
Simbol HTH_Tnp_IS66
Pfam PF13005
Pfam klan CL0123
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
HTH domen
Identifikatori
Simbol HTH_11
Pfam PF08279
Pfam klan CL0123
InterPro IPR013196
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
Tc3 transposaza
Identifikatori
Simbol HTH_Tnp_Tc3_1
Pfam PF11427
Pfam klan CL0123
Dostupne PDB strukture:
Pfam structures
PDB RCSB PDB; PDBe
PDBsum strukturni pregled
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Sekundarna struktura proteina
Heliksi: α-heliks  • 310 heliks  • π-heliks  • β-heliks  • Poliprolinski heliks  • Kolagenski heliks

Ispružena: β-ravan  • Okret  • Beta ukosnica  • Beta izbočina  • α-ravan

Supersekundarna: Upredena zavojnica  • Heliks-okret-heliks  • EF ruka
Aminokiseline
Favorizuju heliks: Metionin • Alanin • Leucin • Glutaminska kiselina • Glutamin • Lizin

Favorizuju izdužene strukture: Treonin • Izoleucin • Valin • Fenilalanin • Tirozin • Triptofan

Favorizuju neuređene strukture: Glicin • Serin • Prolin • Asparagin • Asparaginska kiselina

Bez preferencije: Cistein • Histidin • Arginin
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(1) Osnovni domeni
(1.1) Osnovni leucin rajsferšlus (bZIP)
Aktivirajući transkripcioni faktor (AATF, 1, 2, 3, 4, 5, 6, 7) • AP-1 (c-Fos, FOSB, FOSL1, FOSL2, c-Jun, JUNB, JUND) • BACH (1, 2) • BATF • BLZF1 • C/EBP (α, β, γ, δ, ε, ζ) • CREB (1, 3, L1) • CREM • DBP • DDIT3 • GABPA • HLF • MAF (B, F, G, K) • NFE (2, L1, L2) • NFIL3 • NRL • NRF1 • XBP1
(1.2) Osnovni heliks-petlja-heliks (bHLH)
ATOH1 • AhR • AHRR • ARNT • ASCL1 • BHLHB2 • BMAL (ARNTL, ARNTL2) • CLOCK • EPAS1 • HAND (1, 2) • HES (5, 6) • HEY (1, 2, L) • HES1 • HIF (1A, 3A) • ID (1, 2, 3, 4) • LYL1 • MXD4 • MYCL1 • MYCN • Myogenic regulatorni faktori (MyoD, Myogenin, MYF5, MYF6) • Neurogenini (1, 2, 3) • NeuroD (1, 2) • NPAS (1, 2, 3) • OLIG (1, 2) • Pho4 • Scleraxis • TAL (1, 2) • Twist • USF1
(1.3) bHLH-ZIP
AP-4 • MAX • MITF • MNT • MLX • MXI1 • Myc • SREBP (1, 2)
(1.4) NF-1
NFI (A, B, C, X) • SMAD (R-SMAD (1, 2, 3, 5, 9) - I-SMAD (6, 7) - 4)
(1.5) RF-X
RFX (1, 2, 3, 4, 5, ANK)
(1.6) Osnovni heliks-razmak-heliks (bHSH)
AP-2 (α, β, γ, δ, ε)
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(2) Cink prst DNA-vezujući domeni
(2.1) Nuklearni receptor (Cys4)
podfamilija 1 (Tiroidni hormon (α, β), CAR, FXR, LXR (α, β), PPAR (α, β/δ, γ), PXR, RAR (α, β, γ), ROR (α, β, γ), Rev-ErbA (α, β), VDR)
podfamilija 2 (COUP-TF (I, II), Ear-2, HNF4 (α, γ), PNR, RXR (α, β, γ), Testikularni receptor (2, 4), TLX)
podfamilija 3 (Steroidni hormon (Androgen, Estrogen (α, β), Glukokortikoid, Mineralokortikoid, Progesteron), Estrogen-vezani (α, β, γ))
podfamilija 4 NUR (NGFIB, NOR1, NURR1) • podfamilija 5 (LRH-1, SF1) • podfamilija 6 (GCNF) • podfamilija 0 (DAX1, SHP)
(2.2) Drugi Cys4
GATA (1, 2, 3, 4, 5, 6) • MTA (1, 2, 3) • TRPS1
(2.3) Cys2His2
Generalni transkripcioni faktori (TFIIA, TFIIB, TFIID, TFIIE, TFIIF (1, 2), TFIIH (1, 2, 4, 2I, 3A, 3C1, 3C2))
ATBF1 • BCL (6, 11A, 11B) • CTCF • E4F1 • EGR (2, 3) • ERV3 • GFI1 • GLI-Kruppel familija (1, 2, 3, REST, S2, YY1) • HIC (1, 2) • HIVEP (1, 2, 3) • IKZF (1, 2, 3) • ILF (2, 3) • KLF (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17) • MTF1 • MYT1 • OSR1 • SP (1, 2, 4, 7) • WT1 • Zbtb7 (7A, 7B) • ZBTB (16, 17, 20, 32, 33, 40) • cink prst (3, 7, 9, 10, 19, 22, 24, 33B, 34, 35, 41, 43, 44, 51, 74, 143, 146, 148, 165, 202, 217, 219, 238, 239, 259, 267, 268, 281, 295, 318, 330, 346, 350, 365, 366, 384, 423, 451, 452, 471, 593, 638, 649, 655)
(2.4) Cys6
HIVEP1
(2.5) Naizmenična kompozicija
AIRE • DIDO1 • GRLF1 • ING (1, 2, 4) • JARID (1A, 1B, 1C, 1D, 2) • JMJD1B
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(3) Heliks-zavoj-heliks domeni
(3.1) Homeodomen
ARX • CDX (1, 2) • CRX • CUTL1 • DBX (1, 2)  • DLX (3, 4, 5) • EMX2 • EN (1, 2) • FHL (1, 2, 3) • HESX1 • HHEX • HLX • Homeobox (A1, A2, A3, A4, A5, A7, A9, A10, A11, A13, B1, B2, B3, B4, B5, B6, B7, B8, B9, B13, C4, C5, C6, C8, C9, C10, C11, C13, D1, D3, D4, D8, D9, D10, D11, D12, D13) • HOPX • IRX (1, 2, 3, 4, 5, 6, MKX) • LMX (1A, 1B) • MEIS (1, 2) • MEOX2 • MNX1 • MSX (1, 2) • NANOG • NKX (2-1, 2-2, 2-3, 2-5, 3-1, 3-2, 6-1, 6-2) • PBX (1, 2, 3) • PHF (1, 3, 6, 8, 10, 16, 17, 20, 21A) • PITX (1, 2, 3) • POU domen (PIT-1, BRN-3: A, B, C, Oktamer transkripcioni faktor: 1, 2, 3/4, 6, 7, 11) • OTX (1, 2) • PDX1 • ZEB (1, 2)
(3.2) Paired box
PAX (1, 2, 3, 4, 5, 6, 7, 8, 9)
(3.3) Fork glava / winged heliks
E2F (1, 2, 3, 4, 5) • FOX proteini (C1, C2, D3, E1, G1, H1, K2, L2, M1, N3, O1, O3, O4, P1, P2, P3)
(3.4) Faktori toplotnog šoka
HSF (1, 2, 4)
(3.5) Triptofan klasteri
ELF (2, 4, 5) • EGF • ELK (1, 3, 4) • ERF • ERG • ETS (1, 2, SPIB) • ETV (1, 4, 5, 6) • FLI1 • Interferon regulatorni faktori (1, 2, 3, 4, 5, 6, 7, 8) • MYB • MYBL2
(3.6) TEA domen
transkripcioni pojačivač faktor (1, 2, 3, 4)
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(4) β-Scaffold faktori sa manjim žljebnim kontaktima
(4.1) Rel homologni region
NF-κB (NFKB1, NFKB2, REL, RELA, RELB) • NFAT (C1, C2, C3, C4, 5)
(4.2) STAT
STAT (1, 2, 3, 4, 5, 6)
(4.3) p53
p53 • TBX (1, 2, 3, 5, 19, 21, 22, Brahiuri, TBR1)
(4.4) MADS kutija
Mef2 (A, B, C, D) • SRF
(4.6) TATA vezujući proteini
TBP • TBPL1
(4.7) Grupa visoke pokretljivosti
HMGB (1, 2, 3) • HNF (1A, 1B) • LEF1 • SOX (1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 18, 21) • SRY • SSRP1 • TCF (3, 4) • TOX (1, 2, 3, 4)
(4.10) Domen hladnog šoka
CSDA, YBX1
(4.11) Runt
CBF (CBFA2T2, CBFA2T3, RUNX1, RUNX2, RUNX3, RUNX1T1)
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(0) Drugi transkripcioni faktori
(0.2) HMGI(Y)
HMGA (1, 2) • HBP1
(0.3) Džep domen
Rb • RBL1 • RBL2
(0.5) AP-2/EREBP-vezani faktori
Apetala 2 • EREBP • B3
(0.6) Razno
ARID (1A, 1B, 2, 3A, 3B, 4A) • CAP • IFI (16, 35) • MLL (2, 3, T1) • MNDA • NFY (A, B, C) • Ro/Sigma
vidi isto transkripcioni faktor/koregulator nedostataka