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(-) Description

Title :  CRYSTAL STRUCTURE OF A NOVEL DNA-BINDING DOMAIN FROM NDT80, A TRANSCRIPTIONAL ACTIVATOR REQUIRED FOR MEIOSIS IN YEAST
 
Authors :  S. P. Montano, M. L. Cote, I. Fingerman, M. Pierce, A. K. Vershon, M. M. Georgiadis
Date :  22 Jul 02  (Deposition) - 06 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transcription Activator, Yeast Protein, Dna-Binding, Meiosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. P. Montano, M. L. Cote, I. Fingerman, M. Pierce, A. K. Vershon, M. M. Georgiadis
Crystal Structure Of The Dna-Binding Domain From Ndt80, A Transcriptional Activator Required For Meiosis In Yeast
Proc. Natl. Acad. Sci. Usa V. 99 14041 2002
PubMed-ID: 12384578  |  Reference-DOI: 10.1073/PNAS.222312199
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NDT80 PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 CODON+
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN, RESIDUES 59-330
    Gene: NDT80
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1M7U)

(-) Sites  (0, 0)

(no "Site" information available for 1M7U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M7U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M7U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M7U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M7U)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YHR124W1YHR124W.1VIII:356564-3584471884NDT80_YEAST1-6276272A:65-325 (gaps)
B:65-323 (gaps)		261
259

(-) Sequences/Alignments

Asymmetric 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
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:249
 aligned with NDT80_YEAST | P38830 from UniProtKB/Swiss-Prot  Length:627

    Alignment length:261
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324 
          NDT80_YEAST    65 VGPPFELVRDYCPVVESHTGRTLDLRIIPRIDRGFDHIDEEWVGYKRNYFTLVSTFETANCDLDTFLKSSFDLLVEDSSVESRLRVQYFAIKIKAKNDDDDTEINLVQHTAKRDKGPQFCPSVCPLVPSPLPKHQIIREASNVRNITKMKKYDSTFYLHRDHVNYEEYGVDSLLFSYPEDSIQKVARYERVQFASSISVKKPSQQNKHFSLHVILGAVVDPDTFHGENPGIPYDELALKNGSKGMFVYLQEMKTPPLIIRG 325
               SCOP domains d1m7ua_ A: DNA-binding domain from NDT80                                                                                                                                                                                                                              SCOP domains
               CATH domains 1m7uA00 A:65-325 p53-like transcription factors                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...eee........eeeeeeeee..ee....eeee....eeeeeeeee...hhhhhhhh.eeeeee....eeeee..eeeeeeeeee....eee.eee...---.........ee...................hhhhh..hhhhheee.hhhhhhhh...hhhhhh...eee..eeeeeeee......------.eeeeeeeeeeeeehhhhh---.....eeeee.....eeeeeeeeeee...eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:65-325 (gaps) UniProt: 1-627 [INCOMPLETE]                                                                                                                                                                                                            Transcript 1
                 1m7u A  65 VGPPFELVRDYCPVVESHTGRTLDLRIIPRIDRGFDHIDEEWVGYKRNYFTLVSTFETANCDLDTFLKSSFDLLVEDSSVESRLRVQYFAIKIKAKNDDDDTEINLVQHTA---KGPQFCPSVCPLVPSPLPKHQIIREASNVRNITKTKKYDSTFYLHRNHVNYEEYGVDSLLFSYPEDSIQKVARYERVQFASSISV------NKHFSLHVILGAVVDPDTF---NPGIPYDELALKNGSKGMFVYLQEMKTPPLIIRG 325
                                    74        84        94       104       114       124       134       144       154       164       174|   |  184       194       204       214       224       234       244       254        |-     | 274       284   |   294       304       314       324 
                                                                                                                                        175 179                                                                                 263    270               288 292                                 


Chain B from PDB  Type:PROTEIN  Length:240
 aligned with NDT80_YEAST | P38830 from UniProtKB/Swiss-Prot  Length:627

    Alignment length:259
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314         
          NDT80_YEAST    65 VGPPFELVRDYCPVVESHTGRTLDLRIIPRIDRGFDHIDEEWVGYKRNYFTLVSTFETANCDLDTFLKSSFDLLVEDSSVESRLRVQYFAIKIKAKNDDDDTEINLVQHTAKRDKGPQFCPSVCPLVPSPLPKHQIIREASNVRNITKMKKYDSTFYLHRDHVNYEEYGVDSLLFSYPEDSIQKVARYERVQFASSISVKKPSQQNKHFSLHVILGAVVDPDTFHGENPGIPYDELALKNGSKGMFVYLQEMKTPPLII 323
               SCOP domains d1m7ub_ B: DNA-binding domain from NDT80                                                                                                                                                                                                                            SCOP domains
               CATH domains 1m7uB00 B:65-323 p53-like transcription factors                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) ----------------------------------------NDT80_PhoG-1m7uB01 B:105-323                                                                                                                                                                                                Pfam domains (1)
           Pfam domains (2) ----------------------------------------NDT80_PhoG-1m7uB02 B:105-323                                                                                                                                                                                                Pfam domains (2)
         Sec.struct. author .....eeeee...eee.........eeeeeeee.eee....eee.....eeeeeeee....hhhhhhhh.eeeeeee..eeeeee..eeeeeeeeee....eee..ee..---------....ee.......hhhhhhhhhh......hhhhhhhheee.hhh........hhhhhh...eee..eeeeeee....----------.eeeeeeeeeeeehhhhh........eeeee.....eeeeeeeeeee...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:65-323 (gaps) UniProt: 1-627 [INCOMPLETE]                                                                                                                                                                                                          Transcript 1
                 1m7u B  65 VGPPFELVRDYCPVVESHTGRTLDLRIIPRIDRGFDHIDEEWVGYKRNYFTLVSTFETANCDLDTFLKSSFDLLVEDSSVESRLRVQYFAIKIKAKNDDDDTEINLVQHT---------CPSVCPLVPSPLPKHQIIREASNVRNITKTKKYDSTFYLHRNHVNYEEYGVDSLLFSYPEDSIQKVARYERVQFASS----------KHFSLHVILGAVVDPDTFHGENPGIPYDELALKNGSKGMFVYLQEMKTPPLII 323
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254     |   -      |274       284       294       304       314         
                                                                                                                                       174       184                                                                         260        271
   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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: P53-like (54)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 | P38830: 1m6u 1mn4 1mnn 2etw 2euv 2euw 2eux 2euz 2evf 2evg 2evh 2evi 2evj

(-) Related Entries Specified in the PDB File

1m6u CRYSTAL STRUCTURE OF A NOVEL DNA-BINDING DOMAIN FROM NDT80, A TRANSCRIPTIONAL ACTIVATOR REQUIRED FOR MEIOSIS IN YEAST, C 2 SPACE GROUP