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(-) Description

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(*TP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*C)- 3'
    ChainsB
    EngineeredYES
    Other DetailsVG1C MSE DNA STRAND 1
    SyntheticYES
 
Molecule 2 - 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*TP*GP*TP*GP*GP*C)- 3'
    ChainsC
    EngineeredYES
    Other DetailsVG1C MSE DNA STRAND 2
    SyntheticYES
 
Molecule 3 - NDT80 PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-6P1
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentNDT80 DNA-BINDING DOMAIN
    GeneNDT80
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2ETW)

(-) Sites  (0, 0)

(no "Site" information available for 2ETW)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ETW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ETW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ETW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ETW)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YHR124W1YHR124W.1VIII:356564-3584471884NDT80_YEAST1-6276271A:33-335 (gaps)303

(-) 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    
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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)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ETW)

(-) 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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NDT80_YEAST | P388301m6u 1m7u 1mn4 1mnn 2euv 2euw 2eux 2euz 2evf 2evg 2evh 2evi 2evj

(-) Related Entries Specified in the PDB File

1m6u STRUCTURE OF NDT80 CORE DNA BINDING DOMAIN
1m7u STRUCTURE OF NDT80 CORE DNA BINDING DOMAIN
1mn4 STRUCTURE OF NDT80 CORE DNA BINDING DOMAIN
1mnn STRUCTURE OF A WILTTYPE COMPLEX OF NDT80 - MSE
2ehi
2ehj
2euv
2euw
2eux
2euz
2evf
2evg
2evh