general:

Activators - protein-DNA interaction

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The sequence specific activators: transcription factors Modular design with a minimum of two

functional domains 1. DBD - DNA-binding domain 2. TAD - transactivation domain

DBD: several structural motifs classification into TF-families

TAD - a few different types Three classical categories

Acidic domains (Gal4p, steroid receptor) Glutamine-rich domains (Sp1) Proline- rich domains (CTF/NF1)

Mutational analyses - bulky hydrophobic more important than acidic Unstructured in free state - 3D in contact with target?

Most TFs more complex Regulatory domains, ligand binding domains etc

N

C

TAD

DB

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TF classification based on structure of DBD

bHelix-Loop-Helix(Max)

Zinc finger

Leucine zipper(Gcn4p)

p53 DBDNFκB

STATdimer

Two levels of recognition1. Shape recognition

An α−helix fits into the major groove in B-DNA. This is used in most interactions

2. Chemical recognitionNegatively charged sugar-phosphate chain involved in electrostatic interactionsHydrogen-bonding is crucial for sequence recognition

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Alternative classification of TFs on the basis of their regulatory role Classification questions

Is the factor constitutive active or requires a signal for activation? Does the factor, once synthesized, automatically enter the nucleus to act

in transcription? If the factor requires a signal to become active in transcriptional

regulation, what is the nature of that signal? Classification system

I. Constitutive active nuclear factors II. Regulatory transcription factors

Developmental TFs Signal dependent

Steroid receptors Internal signals Cell surface receptor controlled

Nuclear Cytoplasmic

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Classification - regulatory function

Brivanlou and Darnell (2002) Science 295, 813 -

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Sequence specific DNA-binding- essential for activators TFs create nucleation sites in promoters for

activation complexes Sequence specific DNA-binding crucial role

Principles of sequence specific DNA-binding

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How is a sequence (cis-element) recognized from the outside?

Electrostaticinteraction

Hydrophobicinteraction

Hydrogen-bonds

Form/geometry

Shape recognition Chemical recognition

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Complementary forms

The dimension of an α−helix fits the dimensions of the major groove in B-DNA

Sidechains point outwards and are ideally positioned to engage in hydrogen bonds

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Direct reading of DNA-sequenceRecognition of form

The dimension of an α-helix fits the dimensions of the major groove in B-DNA

Most common type of interaction

Usually multiple domains participate in recognition dimers of same motif tandem repeated motif Interaction of two different motifs

recognition: detailed fit of complementary surfaces Hydration /vann participates seq specvariation of DNA-structure

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Example

Steroid receptor

434 fag repressor

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DNAs form:B-DNA most common

B-form

Major Minor

wide geometryfits α-helix

Each basepair with unique H-bonding-

pattern

Deep and narrow geometry

Each basepairbinary H-bonding-

pattern

B

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DNAs form:A-form more used in RNA-binding

A-form

Major Minor

Deep and narrow geometry Wide and shallow

A

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How is a sequence (cis-element) recognized from the outside?

Electrostaticinteraction

Hydrophobicinteraction

Hydrogen-bonds

Form/geometry

Shape recognition Chemical recognition

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Next level: chemical recognition - reading of sequence information Negatively charged

sugar-phosphate chain = basis for electrostatic interaction Equal everywhere - no sequence-

recognition Still a main contributer to the

strength of binding

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Odd S. Gabrielsen

Electrostatic interactionEntropy-driven binding

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

- ------

Negative phosphate chainpartially neutralized by acloud of counter ions

Na+

Na+

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

Na

- ------

Counter ions liberatedEntropy-driven binding

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How is a sequence (cis-element) recognized from the outside?

Electrostaticinteraction

Hydrophobicinteraction

Hydrogen-bonds

Form/geometry

Shape recognition Chemical recognition

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Odd S. Gabrielsen

Docked protein side chains exploit the H-bonding possibilities for interaction Hydrogen-bonding is

essential for sequence specific recognition 10-20 x in contact interphase Most contacts in major groove Purines most important

A Zif example

DNA

protein

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Recognition by Hydrogen bonding

A

D A Hydrogen-bonding is a

key element in sequence specific recognition

10-20 x in contact surface

Base pairing not exhausted in duplex DNA, free positions point outwards in the major groove

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Unexploited H-bonding possibilities in the grooves

Point outwards in major groove

Point outwards in minor groove

AT-base pair

GC-base pair

Major groove

Major groove

Minor groove

Minor groove

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A ”bar code” in the grooves

AT-basepair

GC-basepair

Unique ”bar code” in major groove

DAA

A D A

AT-pair [AD-A] ≠ TA-pair [A-DA]GC-pair [AA-D] ≠ CG-pair [D-AA]

AT-basepair

Binary ”bar code” in minor groove

AA

GC-basepair

AAD

AT-pair [A-A] = TA-pair [A-A]GC-pair [ADA] = CG-pair [ADA]

Unique recognitionof a base pair requiresTWO hydrogen bondsIn the major groove

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Interaction: Protein side chain - DNA bp Close up

Amino acid sidechains points outwards from the α-helix and are optimally positioned for base-interaction

Still no ”genetic code” in the form of sidechain-base rules

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A complex network of H-bonds

Example: c-Myb - DNA Protein

DNA

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How is a sequence (cis-element) recognized from the outside?

Electrostaticinteraction

Hydrophobicinteraction

Hydrogen-bonds

Form/geometry

Shape recognition Chemical recognition

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Hydrophobic contact points

Ile

Homeodomains

HD

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The Homeodomain-family: common DBD-structure

Homeotic genes - biology Regulation of Drosophila development Striking phenotypes of mutants - bodyparts move Control genetic developmental program

Homeobox / homeodomain Conservered DNA-sequence “homeobox” in a large

number of genes Encode a 60 aa “homeodomain” A stably folded structure that binds DNA Similarity with prokaryotic helix-turn-helix

3D-structure determined for several HDs Drosophila Antennapedia HD (NMR) Drosophila Engrailed HD-DNA kompleks (crystal) Yeast MATα2

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Homeodomain-family: common DBD-structure and sequence recognition

Major groove contact via a 3 α-helix structure helix 3 enters major groove

(“recognition helix”) helix 1+2 antiparallel across helix 3 16 α-helical aa conserved

9 in hydrophobic core some in DNA-contact interphase

(common docking mechanism?)

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Engrailed

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Antennapedia

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Homeodomain-family: common DBD-structure

Minor groove contacted via N-terminal flexible arm R3 and R5 in engrailed and R7 in MATα2 contact AT

in minor groove R5 conserved in 97% of HDs Deletions and mutants impair DNA-binding

Loop between helix 1 and 2 determines Ubx versus Antp function Close to DNA exposed for protein protein interaction

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HD-paradox: what determines sequence specificity? Drosophila Ultrabithorax (Ubx), Antennapedia (Antp),

Deformed (Dfd) and Sex combs reduced (Scr): closely similar HD, biological rolle very different

Minor differences in DNA-binding in vitro TAAT-motif bound by most HD-factors contrast between promiscuity in vitro and specific effects in vivo

Swaps reveal that surprisingly much of the specificity is determined by the N-terminal arm which contacts the minor groove Swaps: Antp with Scr-type N-term arm shows Scr-type specificity in vivo Swaps: Dfd with Ubx-type N-term arm shows Ubx-type specificity in vivo

N-terminal arm more divergent than the rest of HD R5 and R7 (contacting DNA) are present in both Ubx, Antp, Dfd, and Scr Other tail aa diverge much more

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Solutions of the paradox

Conformational effects mediated by N-term arm Even if the α-helical HDs are very similar, a much larger diversity is found in

the N-terminal arms that contact the minor groove

Protein-protein interaction with other TFs through the N-terminal arm - enhanced affinity/specificity - the basis of combinatorial control MATα2 interaction with MCM1 - cooperative interactions Ultrabithorax- Extradenticle in Drosophila Hox-Pbx1 in mammals

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Combinatorial TFs give enhanced specificity Hox proteins, such as

Drosophila Ultrabithorax, have low DNA-binding specificity by themselves but gain affinity and specificity when they bind together with the homeoprotein Extradenticle (or Pbx1 in mammals).

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N-tail in protein-protein interaction- adopt different conformations

Mat-α2/Mcm-1HD

HD

β

α

Conformation determinedby prot prot interaction

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The partner may also be a linker histone Repression of the mouse

MyoD gene by the linker histone H1b and the homeodomain protein Msx1.

The first evidence that a linker histone subtype operates in a gene-specific fashion to regulate tissue differentiation

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It works impressively well

Hox genes

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Homeobox families

Hox genes Hox genes govern developmental pathways along the

anterior–posterior axis In mammalian species, there are 39 Hox genes

organised in four clusters labelled A, B, C and D located on four different chromosomes and numbered from 1 to 13, although no cluster contains a full set.

38

POU family

HD HD

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POU-family: common DBD-structure

The POU-name : Pit-1 pituitary specific TF Oct-1 and Oct-2 lymphoide TFs Unc86 TF that regulates neuronal development in C.elegans

A bipartite160 aa homeodomain-related DBD a POU-type HD subdomain (C-terminally located) et POU-specific subdomain (N-terminally located) Coupled by a variabel linker (15-30 aa)

POU is a structurally bipartite motif that arose by the fusion of genes encoding two different types of DNA-binding domain.

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POU: Two independent subdomains

POUHD subdomain 60 aa closely similar to the classical HD Only weakly DNA-binding by itself (<HD) contacts 3´-half site (Oct-1: ATGCAAAT) docking similar to engrailed. Antp etc Main contribution to non-specific backbone contacts

POUspec subdomain 75 aa POU-specific domain enhances DNA-affinity 1000x contacts 5´-half site (Oct-1: ATGCAAAT) contacts opposite side of DNA relative to HD structure similar to prokaryotic λ- and 434-repressors

The two-part DNA-binding domain partially encircles the DNA.

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Flexible DNA-recognition

POU-domains have intrinsic conformational flexibility and this feature appears

to confer functional diversity in DNA-recognition

The subdomains are able to assume a variety of conformations, dependent on the DNA element.

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Flexibility

On the natural high-affinity Oct-1 octamer (ATGCAAAT) binding site, the two Oct-1 POU-subdomains lie on opposite sides of the DNA

The unstructured linker permits flexible subdomain positioning and hence diversity in Oct-1 sequence recognition.

Myb family TFs

44

HD HD HD

DBD signature

* . :: :: . : * : : : :**::**:::: **.: * ::* .:* .: **:: ***:** :**.*:*:**********:*****:***.*:*::********:**************:***:.*** *** * .*** :********MYBB_HUMAN MSRRTR------CEDLDELHYQDTDSDVPEQR---DSKCKVKWTHEEDEQLRALVRQFGQQDWKFLASHFPNRTDQQCQYRWLRVLNPDLVKGPWTKEEDQKVIELVKKYGTKQWTLIAKHLKGRLGKQCRERWHNHLNPEVKKSCWTEEEDRIICEAHKVLGNRWAEIA 161MYBB_CHICK MARRSR------GEDQDELHCQDTDSDVPEQR---DGRCKVKWTQEEDEQLKMLVRHYGQNDWKFLASHFPNRSDQQCQYRWLRVLNPDLVKGPWTKEEDQKVIELVKKYGTKQWTLIAKHLKGRLGKQCRERWHNHLNPEVKKSSWTEEEDRIIFEAHKVLGNRWAEIA 161 MYB_rat METGPH-----SEDEDDDLQYADHDYEVPQQKGLKKLWNRVKWTRDEDDKLKKLVEQHGTDDWTLIASHLQNRSDFQCQHRWQKVLNPELIKGPWTKEEDQRVIELVQKYGPKRWSLIAKHLKGRIGKQCRERWHNHLNPEVKKSSWTEEEDRIIYEAHKRLGNRWAEIA 165MYBA_HUMAN MAKRSR-----SEDEDDDLQYADHDYEVPQQKGLKKLWNRVKWTRDEDDKLKKLVEQHGTDDWTLIASHLQNRSDFQCQHRWQKVLNPELIKGPWTKEEDQRVIELVQKYGPKRWSLIAKHLKGRIGKQCRERWHNHLNPEVKKSSWTEEEDRIIYEAHKRLGNRWAEIA 165MYBA_CHICK MAKRPR-----TSEEDDDFQYADHDYEISQQRSLKKICNRVKWTRDEDEKLKKLVEQNGTDDWAFIASHLQNRSDFQCQHRWQKVLNPELIKGPWTKEEDQRVIELVQKYGPKRWSLIAKHLKGRIGKQCRERWHNHLNPEVKKSSWTEAEDRVIYEAHKRLGNRWAEIA 165MYBA_XENLA MAGRAR-----SEDEEEDGQFTEHDYDVSLQKGPKKPWSKLRWTKDEDDKVKKLVEKHG-EDWGVVARHFINRSEVQCQHRWHKVLSPELVKGPWTKEEDQRVIELVHKYGPKKWSIIAKHLKGRIGKQCRERWHNHLNPDVKKSSWTEEEDRIIYSAHKRMGNRWAEIA 164 MYB_HUMAN MARRPRHSIYSSDEDDEDFEMCDHDYDGLLPKSGKRHLGKTRWTREEDEKLKKLVEQNGTDDWKVIANYLPNRTDVQCQHRWQKVLNPELIKGPWTKEEDQRVIELVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLNPEVKKTSWTEEEDRIIYQAHKRLGNRWAEIA 170 MYB_CHICK MARRPRHSIYSSDDDEEDVEMYDHDYDGLLPKAGKRHLGKTRWTREEDEKLKKLVEQNGTEDWKVIASFLPNRTDVQCQHRWQKVLNPELIKGPWTKEEDQRVIELVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLNPEVKKTSWTEEEDRIIYQAHKRLGNRWAEIA 170 MYB_XENLA MDRRP--SQYSSEEEDDEIEMYEHDYDGLLSK-GKRHLGKTRWTREEDEKLKKLVEQNGTEEWKVIASFLPNRTDVQCQHRWQKVLNPELIKGPWTKEEDQRVIELVHKYGPKRWSVIAKHLKGRIGKQCRERWHNHLNPEVKKSSWTEEEDRTIYEAHKRLGNRWAEIA 167 ruler 1.......10........20........30........40........50........60........70........80........90.......100.......110.......120.......130.......140.......150.......160.......170

*:*******::*******::** : *:*.: . . . . . * : * * .: :MYBB_HUMAN KMLPGRTDNAVKNHWNSTIKRKVDTGGFLSESKDCKPPVYLLLELEDKDGLQSAQPTEGQGSLLTNWPSVPPTIKEEENSEEELAAATTSKEQ--EPIGTDLDAVRTPEPLEEFPKREDQEGSPPETSLPYKWVVEAANLLIPAVGSSLSEALDLIESDPDAWCDLSKFD 329MYBB_CHICK KLLPGRTDNAVKNHWNSTIKRKVDTGGFLNETKESQP-LYLLVEVDDNESQSGTRAES--QTIVPNWPVDISEIKEEDVSDE---EVTGLQELPSELPAADLAEHNEEGTPDDV----VPEDASASVASPYKWVVEAANYLCPTSVPALNEALDMIESDPDGWCDLTQFD 321 MYB_rat KLLPGRTDNSIKNHWNSTMRRKVEQEGYLQDGIKS--ERS-SSKLQHKPCVTEQCKGEIKCDMKKYVGLKYHGRVPWKCEEIPGYQYVSP-------------DGNCVEHVQ-TSAFIQQPFVDED-PDKEKKIKELELLLMSAENEVRRKRLPPQ---PGSFSSWSGSF 314MYBA_HUMAN KLLPGRTDNSIKNHWNSTMRRKVEQEGYLQDGIKS--ERS-SSKLQHKPCAAMD---HMQTQNQFYIPVQ-----------IPGYQYVSP-------------EGNCIEHVQPTSAFIQQPFIDED-PDKEKKIKELEMLLMSAENEVRRKRIPSQ---PGSFSSWSGSF 301MYBA_CHICK KLLPGRTDNSIKNHWNSTMRRKVEQEGYLQDGTKSSSERTGSSTLAQKPCVTME---HLHTQNQFYIPVQT---------HIPVYQYASP-------------EDSCIEHASASANLVQQSFIDDD-PDKEKKIKELELLLMSTENEIRRKRLSSQ---AGSLPGWSGSF 306MYBA_XENLA KLLPGRTDNSIKNHWNSTMKRKVEQEGYLQDLMNC--DRP--SKLQAKSCAAPN---HLQAQNQFYIPVQT---------QIPRYSSLSH-------------DDNCIEIQN-SFSFIQQPFVDADDPEKEKRIKELELLLMSAENEVRRKRVPS-----GSSLTWSESY 299 MYB_HUMAN KLLPGRTDNAIKNHWNSTMRRKVEQEGYLQESSKASQPAVATSFQKNSHLMGFA---QAPPTAQLPATGQPT-----VNNDYSYYHISEAQNVSSHVPYPVALHVNIVNVPQPAAAAIQRHYNDED-PEKEKRIKELELLLMSTENELKGQQVLPTQNHTCSYPGWHSTT 331 MYB_CHICK KLLPGRTDNAIKNHWNSTMRRKVEQEGYLQESSKAGLPSATTGFQKSSHLMAFA---HNPPAGPLPGAGQAP-----LGSDYPYYHIAEPQNVPGQIPYPVALHVNIVNVPQPAAAAIQRHYNDED-PEKEKRIKELELLLMSTENELKGQQALPTQNHTANYPGWHSTT 331 MYB_XENLA KLLPGRTDNAIKNHWNSTMRRKEEQEGYLQNSSKTNQHTIVTNFPKSNHLMTFT---HTRASAEHSQAS---------TSSFPYYHIAEHQNAS----YPVALRVNIVNVPQLATAPVQRHYNDED-PEKEKRIKELELLLMSTENEINQKQEL--LNHTASYTTCHSTT 318 ruler .......180.......190.......200.......210.......220.......230.......240.......250.......260.......270.......280.......290.......300.......310.......320.......330.......340

. : : : : . . : . : :.MYBB_HUMAN LPEEPSAEDSINNSLVQLQASHQQQVLPPRQPSALVPSVTEYRLDGHTISDLSRSSRGELIPISPSTEVGGSGIGTPPSVLKRQRKRRVALSPVTEN------------------------------------------------------------------------- 426MYBB_CHICK LPEEPSAGSSSSSNSPVRQT--------PSKPTPSLPNVTEYRLDGHTISDLSKSRKGELIPISPHAEVS---FGTPPSVLKRQKKRKISLSPVTENA------------------------------------------------------------------------ 408 MYB_rat LMDDSMSN--------------------------TLNNLEEHTTEFYSMDENQTVSAQQN-SPTKFLAVEANAVLSSLQTIPEFAETLELIESDPVAWSDVTSFDLSDAAASPVKSTPVKLMRIQHNEGAMECQFNVSLVLEGKKNSCNGGDSEAIPLASPNVVKFSTPP 457MYBA_HUMAN LMDDNMSN--------------------------TLNSLDEHTSEFYSMDENQPVSAQQN-SPTKFLAVEANAVLSSLQTIPEFAETLELIESDPVAWSDVTSFDISDAAASPIKSTPVKLMRIQHNEGAMECQFNVSLVLEGKKNTCNGGNSEAVPLTSPNIAKFSTPP 444MYBA_CHICK VMEDCVPN--------------------------TLNSLGEQTSEFYSMDETQGTSVQQN-SPTKYLAVEANAVLSSLQTIPEFAETLELIESDPLAWSDVTSFDLSEAVASPVKPAPLKLMRIQHNERAAECQFNVSVMLDGKKHSSISGEEEAVFPTTPNLTKYSTPP 449MYBA_XENLA HMGESMSN--------------------------TMSHLEEQTHDFYSLDEIPNTSGQQS-VEDKILAPEANIVLQPLETIPEFSETLELIDVDTVDWNNIESFELP-FTASPAKHTPMKWI----HEISPECALNSCLVQADGR-----GSASRVLSSSPAMPKFYSPP 432 MYB_HUMAN IADHTRPHGDSA----------------------PVSCLGEHH-STPSLPADPGSLPEESASPARCMIVHQGTILDNVKNLLEFAETLQFIDS----------------------------------------------------------------------------- 401 MYB_CHICK VADNTRTSGDNA----------------------PVSCLGEHHHCTPSPPVDHGCLPEESASPARCMIVHQSNILDNVKNLLEFAETLQLIDS----------------------------------------------------------------------------- 402 MYB_XENLA IGGNPRLHGQST----------------------PDSCLGDPHHSTPSPQVDHSCLPEESASPARYFGVN---LLIQMKNLAEYSET-QLIDS----------------------------------------------------------------------------- 385 ruler .......350.......360.......370.......380.......390.......400.......410.......420.......430.......440.......450.......460.......470.......480.......490.......500.......510

::. : ::: .:****: . :* * .: :: . :*. : ** : : :*:******:** :**:: :. .: **: :*::.*: . :: *MYBB_HUMAN -----------------STSLSFLDSCNSLTPKSTPVKTLPFSPSQFLNFWNKQDTLELESPSLTSTPVCS-QKVVVTTPLHRDKTPLHQKH-AAFVTPDQK-YSMDNTPHTPTPFKNALEK----YGPLKPLPQTP-HLEEDLKEVLRSEAGIELIIEDD--IRPEKQK 569MYBB_CHICK ----------------PSTSLSFLDSCNSMTPKSTPVKTLPFSPSQFLNFWTKQDTLELENPSLTSTPVCS-QKVIVTTPLHRDKTPLLQKN-SAFVTPDQK-YVVDNTPHTPTPFKNALEK----YGPIRPLPQTP-HLEEDLKEVLRSEAGIELIIEDD--VKPHKQK 552 MYB_rat TILRKKKRLRVGQSAGSELGEGSLSEGNNAALKHTPVKTLPFSPSQFFNTCPGSEQLNIENPSFTSTPICG-QKVLITTPLQKEATPKDQKENVGFRTPTIRRSILGTTPRTPTPFKNALAAQEKKYGPLKIVSQPLAFLEEDIREVLKEETGTDIFLKEE---DEPAYK 623MYBA_HUMAN AILRKKRKMRVGHSPGSELRDGSLNDGGNMALKHTPLKTLPFSPSQFFNTCPGNEQLNIENPSFTSTPICG-QKALITTPLHKETTPKDQKENVGFRTPTIRRSILGTTPRTPTPFKNALAAQEKKYGPLKIVSQPLAFLEEDIREVLKEETGTDLFLKEE---DEPAYK 610MYBA_CHICK AILRKKKRLRAGQSPVNELNDGLCNDAINVALKHTPVKTLPFSPSQFFNTCSGNEQFNLENPAFTSTPICG-QKVLITTPLHKETTPTDQKENAGFRTPTIRRSLLGSTPRTPTPFKNALAAQEKKYGPLKLTSQPLAFLEEDIREVLKEETGTDIFLKEE---DDSVYK 615MYBA_XENLA TILRKKK-IHPDLSLTPEVR-----DASNVVLKGTPVKTRQYSPLQLFRSGNVQNHLNLDNLPLTSTPVCG-QKISAT-PLQRQITPKKDKENAGFRTPTIRRSLMAVTPRTPTPFKNALAAQEKKYGPLRTVMQPLIFVEEDIMEVLKKETEKDVFIKEE---KESDCK 591 MYB_HUMAN ----------------------------------------------FLNTSSNHENSDLEMPSLTSTPLIG-HKLTVTTPFHRDQTVKTQKENTVFRTPAIKRSILESSPRTPTPFKHALAAQEIKYGPLKMLPQTPSHLVEDLQDVIKQESDESGIVAEFQENGPPLLK 524 MYB_CHICK ----------------------------------------------FLNTSSNHENLNLDNPALTSTPVCG-HKMSVTTPFHRDQPFKTQKENHVFRTPAIKRSILESSPRTPTPFKNALAAQEIKYGPLKMLPQTPTHLVEDLQDVIKQESEESAIVAGLHESGPPLLK 525 MYB_XENLA ----------------------------------------------FLNTSTQHENLEMEHQSLTSTPICASQKNTITTSLLRDHALRLQKENHLLRTPAIKRSILNSTPRTPTPFKNALAAQEFKHGPLKLLHHTPLHLAEDIQEVIKQETDESGIVHDHCNTEEPLLK 509 ruler .......520.......530.......540.......550.......560.......570.......580.......590.......600.......610.......620.......630.......640.......650.......660.......670.......680

:. * : : : : . . . . : . *. . .:* .: : : *::MYBB_HUMAN RKPGLRRSPIKKVRKSLALDIVDEDVKLMMSTLPKSLSLPTTAPS----NSSSLT-LSGIKE---------DNSLLNQGFLQAKPEKAAVAQKPRSHFTTPAPMSSAWKTVACGGTRDQLFMQEKARQLLG-RLKPSHT-SRTLILS 700MYBB_CHICK RKQGLRRSPIKKVRKSLALDIVDEDMTQNMPALPKTICFKRTQPVNFLSRSLNLS-SSNRKN---------DSGLLNRAFVQVQSEKMSYRKMP-SHFRPPAPMTRAWKAVACGGTQDQLFMQEKARQFLG-TLKQSHT-SRTLILS 686 MYB_rat SCKQEHSASVKKVRKSLALESWDKE-EPGTQLLTEDIS-DMQSENILTTSLLMIPLLEIHDNRCNLTPEKQDINSANKTYTLTKKRPNPNTCKAV-KLEKSLQSNCEWETVVYGKTEDQLIMTEQARRYLSTYTAPSST-SRALIL- 765MYBA_HUMAN SCKQENTASGKKVRKSLVLDNWEKE-ESGTQLLTEDIS-DMQSENRFTTSLLMIPLLEIHDNRCNLIPEKQDINSTNKTYTLTKKKPNPNTSKVV-KLEKNLQSNCEWETVVYGKTEDQLIMTEQARRYLSTYTATSST-SRALIL- 752MYBA_CHICK SCKQEHNSS-KKVRKSLVLDAWEKE-ELGAQLFTEDSGLDVQSENAYTTSLLMIPLLEIHDNRCNLPSENQDTNSSNKANAVIKKKLNACSSKNI-KLEKSLQPNYEWEAVVYGKTEDQLIMTEQARRYLNAYTATSNT-SRALIL- 757MYBA_XENLA PMKQEHVSTVRKVRKSLILDSCDKE-ELGADFLAPDEVSQSQNGNTLPTSFLMIPLGERQDQKC-------DENTDTRKGSVMQRKNYIPATRNV-KLQSSVQPLCEWEAVVYGKTEDQLIMTEQARRYLDTYKPTSSSGLRHLIL- 728 MYB_HUMAN KIKQEVESPTDKSGNFFCSHHWEGD-SLNTQLFTQTSPVADAPN-ILTSSVLMAPASE-------------DEDNVLKAFTVPKNRSLASP---------LQPCSSTWEPASCGKMEEQMTSSSQARKYVNAFSA------RTLVM- 640 MYB_CHICK KIKQEVESPTDKAGNFFCSNHWEGE-NLNTQLFTHASTMEDVPN-LLTSSILKMPVSE-------------EEGSFHKAFAVPRNRPLASP---------MQHLNNAWESASCGKTEDQMALTDQARKYMAAFPT------RTLVM- 641 MYB_XENLA RIKQEVESPTHKVGNLYFSSYWEGE-SLNAQLFRQQSTLDDTSNSILTSSLLMKPVSE-------------KEDHIFKSFPVQSIKSYTSP---------LQHLSGTWDVMSCSRMEDQKILAEQYCKYIKNFS--------TLVI- 624 ruler .......690.......700.......710.......720.......730.......740.......750.......760.......770.......780.......790.......800.......810.......820.......

DBD

TAD

FAETL

TP

EVES

$

$ P

IV.VSBM?

Å Å

K438AcK441Ac

K527$S532Phospho

K503$

Å Å Å

K467Ac K476AcK481Ac

Sano (2001) Tomita (2000)

Versjon 6 -- RAa 7-OCT-2005

OSG et al

W W W W W W W W

W

R1 R2 R3

Trp-rich pseudorepeats

HTH-related motifs3 α-helices in each repeat

R2

R3

3D DBD

R2 R3

c-Myb

DNA-binding domainControls blood cell development

Subject to oncogenic activation