2ETW | PD0727 - JenaLib

Title :   PRINCIPLES OF PROTEIN-DNA RECOGNITION REVEALED IN THE STRUCTURAL ANALYSIS OF NDT80-MSE DNA COMPLEXES

Authors :   J. S. Lamoureux, J. N. Glover

Date :   27 Oct 05 (Deposition) - 21 Mar 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.67

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Beta Sandwich, Ig-Fold, B-Dna, Cell Cycle/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. S. Lamoureux, J. N. Glover
Principles Of Protein-Dna Recognition Revealed In The Structural Analysis Of Ndt80-Mse Dna Complexes.
Structure V. 14 555 2006
PubMed-ID: 16531239 | Reference-DOI: 10.1016/J.STR.2005.11.017
(for further references see the PDB file header)

Compounds

*Molecule 1 - 5'-D(TPGPCPCPAPCPAPCPAPAPAPAPAPC)- 3'*
	Chains	:	B
	Engineered	:	YES
	Other Details	:	VG1C MSE DNA STRAND 1
	Synthetic	:	YES

*Molecule 2 - 5'-D(APGPTPTPTPTPTPGPTPGPTPGPGPC)- 3'*
	Chains	:	C
	Engineered	:	YES
	Other Details	:	VG1C MSE DNA STRAND 2
	Synthetic	:	YES

Molecule 3 - NDT80 PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEX-6P1
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	NDT80 DNA-BINDING DOMAIN
	Gene	:	NDT80
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (1, 1)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:297
 aligned with NDT80_YEAST | P38830 from UniProtKB/Swiss-Prot  Length:627

    Alignment length:303
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332   
          NDT80_YEAST    33 VILTQLNEDGTTSNYFDKRKLKIAPRSTLQFKVGPPFELVRDYCPVVESHTGRTLDLRIIPRIDRGFDHIDEEWVGYKRNYFTLVSTFETANCDLDTFLKSSFDLLVEDSSVESRLRVQYFAIKIKAKNDDDDTEINLVQHTAKRDKGPQFCPSVCPLVPSPLPKHQIIREASNVRNITKMKKYDSTFYLHRDHVNYEEYGVDSLLFSYPEDSIQKVARYERVQFASSISVKKPSQQNKHFSLHVILGAVVDPDTFHGENPGIPYDELALKNGSKGMFVYLQEMKTPPLIIRGRSPSNYASSQ 335
               SCOP domains d2etwa_ A: DNA-binding domain from NDT80                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2etwA00 A:33-335 p53-like transcription factors                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eeee...........hhhhh......eeeee...eee.........eeeeeeee..eee..eeeee....eeeeeeee....hhhhhhhh.eeee........eee..eeeeeeeeee.....ee.eeee..hhhhh.ee....ee.......hhhhhhhh....hhhhhhhhhhhheee.hhhhhhhh...hhhhhh...eee..eeeeeeee...............eeeeeeeeeee...------....eeeee.....eeeeeeeeeee...eeee..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:33-335 (gaps) UniProt: 1-627 [INCOMPLETE]                                                                                                                                                                                                                                                      Transcript 1
                 2etw A  33 VILTQLNEDGTTSNYFDKRKLKIAPRSTLQFKVGPPFELVRDYCPVVESHTGRTLDLRIIPRIDRGFDHIDEEWVGYKRNYFTLVSTFETANCDLDTFLKSSFDLLVEDSSVEGRLRVQYFAIKIKAKNDDDDTEINLVQHTAKRDKGPQFCPSVCPLVPSPLPKHQTIREASNVRNITKMKKYDSTFYLHRDHVNYEEYGVDSLLFSYPEDSIQKVARYERVQFASSISVKKPSQQNKHFSLHVILGAVVDPD------PGIPYDELALKNGSKGMFVYLQEMKTPPLIIRGRSPSNYASSQ 335
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282   |     -|      302       312       322       332   
                                                                                                                                                                                                                                                                                       286    293

Chain B from PDB  Type:DNA  Length:13
                                             
                 2etw B   2 GCCACACAAAAAC  14
                                    11

Chain C from PDB  Type:DNA  Length:14
                                              
                 2etw C   1 AGTTTTTGTGTGGC  14
                                    10

Legend:		→ Mismatch	(orange background)
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		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NDT80_YEAST | P38830)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0051321	meiotic cell cycle	Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000228	nuclear chromosome	A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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