Yeast Tfiia/TBP/DNA Complex

1YTF (PDB)

The complex contains 4 protein chains - all engineered fragments - and a segment of DNA containing the Tata Box.
     Tata-Box Binding Protein (TBP) in the structure consists of the C-Terminal 188 aa's. (Chain A)
     Transcription Factor Iia (Tfiia) in the structure consists of the conserved residues (Chains B,C,D) Nonconserved residues 56 -209 were omitted.
     Cyc1 Tata-Box DNA in the structure consists of Nucleotides -129 to -114 from the Cyc1 translation start site

The DNA sequence contains the Tata box. The nucleic acid colored by residue. A, T, G, C are red, blue, green, yellow respectively. The f chain is al lighter tint. The hydrogen bonds are between base pairs as well as in the protein binding site.

The complete complex. The A chain with the Tata binding site is shown in black space fill to indicate the groove. Note that everything in the binding site is A or T. The bases of the two chains are spread sidewise rather than in a base paired helix. The B, C and D chain are shown as H bodned backbones toe illustrate the secondary structure.

Secondary Structure

The hydrogen bonding from the sequence is shown above in white.
According to the Secondary Structure Elements (Kabsch & Sander) in the PDR
Chain A (black) has 4 alpha helices and 7 beta pleated sheets (extended).
Chain B (gold) has 3 alpha helices.
Chain C (white) has 7 beta pleated sheets (extended).
Chain D (yellow) has 2 alpha helices and 7 beta pleated sheets (extented).

SCOP and CATH Classification

The SCOP classification for 1YTF includes three classes, butthe folds, superfamily and family are restricted to this protein.

Class	Fold	Superfamily	Family	Protein
Alpha and beta proteins (a+b)	TBP-like beta-alpha-beta(4)-alpha	TATA-box binding protein-like	TATA-box binding protein (TBP), C-terminal domain duplication: consists of two clear structural repeats	TATA-box binding protein (TBP), C-terminal domain structure of the N-terminal domain is not known yet
All beta proteins	Transcription factor IIA (TFIIA), N-terminal domain barrel, closed; n=6, S=12; mixed beta-sheet	Transcription factor IIA (TFIIA), N-terminal domain dimer of non-identical beta-sheet subunits	Transcription factor IIA (TFIIA), N-terminal domain	Transcription factor IIA (TFIIA), N-terminal domain
All alpha proteins	Transcription factor IIA (TFIIA), N-terminal domain 4 helices; bundle, closed, right-handed twist	Transcription factor IIA (TFIIA), N-terminal domain dimer of non-identical alpha-hairpin subunits	Transcription factor IIA (TFIIA), N-terminal domain	Transcription factor IIA (TFIIA), N-terminal domain

The CATH classification for 1YTF includes 6 folds. The 1ytfA1 and the 1ytfA2 domains are illustrated below. The CATH classification is 3.30.310.10

Experimental

X-ray diffraction
R-factor 0.235
Synchontron, EMBL, Beamline X11
Space group P 21 21 21
Gaps in PDB entry
Resolution 2.50
Unit cell dimensions a 59.15 b 93.05 c 117.83

Structure Alignment - 1YTF:A Neighbors

Structural neighbors:

1TGH    Tata Binding Protein, Human
1AIS      Tata Binding Protein from Pyrocossus Woesei (Archeae)
1E42     Beta2 Adaptin Appendage Domain
1APS     Acylphosphatase

1YTF Secondary Structure adn Sequence from the PDB
1 SGIVPTLQNI VATVTLGCRL DLKTVALHAR NAEYNPKRFA AVIMRIREPK
EE EE EEEEE SS HHHHHHHSS SEEE TTT S SEEEEEETTE

51 TTALIFASGK MVVTGAKSED DSKLASRKYA RIIQKIGFAA KFTDFKIQNI
EEEEE TTSE EEEE BSSHH HHHHHHHHHH HHHHHHT B EE EE

101 VGSCDVKFPI RLEGLAFSHG TFSSYEPELF PGLIYRMVKP KIVLLIFVSG
EEEEE SS B HHHHHHHTT TTEE TTT SSEEEEETTT TEEEEE TTS

151 KIVLTGAKQR EEIYQAFEAI YPVLSEFRKM
EEEEE BSSH HHHHHHHHHH HHHHHHTB

The structure alignment aligned the extended pleated sheet (VATV) , the helix (LKTV) for all five structures. For four of the five structures a pleated sheet and turns (NAEY & PKR) and a bend and a extended beta sheet were aligned (AVIMRIRE). Single amino acids that are ajacent to an area of secondary structure are frequently aligned, e.g. the D before LKTV.

  1YTF:A    1/62    SGIVPTLQNIVATVTLGCRL-DLKTVALHAR----NAEYNPKR--FAAVIMRIRE---PK

  1TGH:A    5/156   SGIVPQLQNIVSTVNLGCKL-DLKTIALRAR----NAEYNPKR--FAAVIMRIRE---PR

  1AIS:A    5/6     SKVKLRIENIVASVDLFAQL-DLEKVLDLCP----NSKYNPEE--FPGIICHLDD---PK

  1E42:A  169/849   ---------NELQFQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKLTNGIW

  1APS:_    4/5     ------RPLKSVDYEVFGRV-QGVCFRMYAE----D---------------EARK---IG

  1YTF:A   51/112   TTALIF----A----SGKMVVTGAKSEDDSKLASRKYARIIQKIGFAA-KFTDFKIQNIV

  1TGH:A   55/206   TTALIF----S----SGKMVCTGAKSEEQSRLAARKYARVVQKLGFPA-KFLDFKIQNMV

  1AIS:A   55/56    VALLIF----S----SGKLVVTGAKSVQDIERAVAKLAQKLKSIGVKFKRAPQIDVQNMV

  1E42:A  220/900   ILAELR----IQPGNPNYTLSLKCRAPEVSQYIYQVYDSILKN-----------------

  1APS:_   35/36    VVGWVKNTSKG----TVTGQVQGP--EEKVNSMKSWLSKVGSPSSRID-RTNFSNEKTIS

  1YTF:A  102/163   GSCDVKFPIRLEGLAFSHG-TFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKQR

  1TGH:A  106/257   GSCDVKFPIRLEGLVLTHQQ-FSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVR

  1AIS:A  107/108   FSGDIGREFNLDVVALTLP--NCEYEPEQFPGVIYRVKEPKSVILLFSSGKIVCSGAKSE

  1E42:A            ------------------------------------------------------------

  1APS:_   88/89    K-----------------------------------------------------------

  1YTF:A  161/222   EEIYQAFEAIYP

  1TGH:A  165/316   AEIYEAFENIYP

  1AIS:A  165/166   ADAWEAVRKLLR

  1E42:A            ------------

  1APS:_            ------------

1TGH:A

0.7	82.5
171	7.1

1AIS:A

1.9	40.4
171	6.9

1.9	38.6
171	-1.0

1E42:A

2.6	7.9
76	4.6

2.6	6.6
76	-1.0

2.4	5.3
76	-1.0

1APS:_

3.7	8.6
81	4.2

3.8	7.4
81	-1.0

3.6	7.4
81	-1.0

3.9	3.3
61	-1.0

1YTF:A

1TGH:A

1AIS:A

1E42:A

Each cell in distance matrix provides:

RMSD(Å)	Sequence identity(%)
Length of alignment	Z-score

Pairwise sequence alignment

The sequence alignment did aligned the extended pleated sheet (VATV) for the first four sequence. It aligned the helix (LKTV) for all five structures.The two amino acids before that stretch are conserved: Lor V followed by D or E. The sequences also align for the pleated sheet (NAEY) with the Y occuring in four of the sequences (F in the fifth). The PKR turn aligns and followed by F in four of the sequnces Y in the fifth. The AVIMRIRE stretch contains a gap in the sequence alignment.

1YTF_A          -----------SGIVPTLQNIVATVT-------------LGCRLDLKTVALHARNAEYNP 36
1TGH_A          -------GSRGSGIVPQLQNIVSTVN-------------LGCKLDLKTIALRARNAEYNP 40
1AIS_A          -------MVDMSKVKLRIENIVASVD-------------LFAQLDLEKVLDLCPNSKYNP 40
1E42_A          MGSSHHHHHHSSGLVPRGSHMGMAPGGYVAPKAVWLPAVKAKGLEISGTFTHRQGHIYME 60
1APS__          -----------STARP------------------------LKSVDYE-VFGRVQGVCFR- 23
                           *      .    :                   :: .       .  : 

1YTF_A          KRFAAVIMR------IREPKTTALIFASGKMVVTGAKSEDDSKLASRKYARIIQKIGFAA 90
1TGH_A          KRFAAVIMR------IREPRTTALIFSSGKMVCTGAKSEEQSRLAARKYARVVQKLGFPA 94
1AIS_A          EEFPGIICH------LDDPKVALLIFSSGKLVVTGAKSVQDIERAVAKLAQKLKSIGVKF 94
1E42_A          MNFTNKALQHMTDFAIQFNKNSFGVIPSTPLAIHTPLMPNQSIDVSLPLNTLGPVMKMEP 120
1APS__          -MYAEDEAR-------KIGVVGWVKNTSKGTVTGQVQGPEEK---VNSMKSWLSKVGSPS 72
                  :.    :                 .*   .       ::              : 

1YTF_A          K-FTDFKIQN----------------IVGSCDVK-----------------------FPI 110
1TGH_A          K-FLDFKIQN----------------MVGSCDVK-----------------------FPI 114
1AIS_A          KRAPQIDVQN----------------MVFSGDIG-----------------------REF 115
1E42_A          LNNLQVAVKNNIDVFYFSCLIPLNVLFVEDGKMERQVFLATWKDIPNENELQFQIKECHL 180
1APS__          S---RIDRTN----------------FSNEKTIS------------------------KL 89
                     .   *                :  .  :                          :

1YTF_A          RLEGLAFSHGTFSSYEPEL--FPG--LIYRMVKPKIVLLIFVSGKIVLTG----AKQREE 162
1TGH_A          RLEGLVLTHQQFSSYEPEL--FPG--LIYRMIKPRIVLLIFVSGKVVLTG----AKVRAE 166
1AIS_A          NLDVVALTLPN-CEYEPEQ--FPG--VIYRVKEPKSVILLFSSGKIVCSG----AKSEAD 166
1E42_A          NADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKLTNGIWILAELRIQPGNPNYTLSLKCR 240
1APS__          EYSNFSVRY--------------------------------------------------- 98
                . . .                  .        .         .      .     . 

1YTF_A          IYQAFEAIYPVLSEFRKM- 180
1TGH_A          IYEAFENIYPILKGFRKTT 185
1AIS_A          AWEAVRKLLRELDKYL--- 182
1E42_A          APEVSQYIYQVYDSILKN- 258
1APS__          -------------------

Start of Multiple Alignment
There are 4 groups
Aligning...
Group 1:                     Delayed
Group 2: Sequences:   2      Score:3587
Group 3: Sequences:   3      Score:2602
Group 4:                     Delayed
Sequence:4     Score:1309
Sequence:5     Score:347
Alignment Score 1202