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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MATA1/MATALPHA2 HOMEODOMAIN HETERODIMER BOUND TO DNA
 
Authors :  T. Li, M. R. Stark, A. D. Johnson, C. Wolberger
Date :  02 Nov 95  (Deposition) - 29 Jan 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Complex, Dna-Binding Protein, Dna, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Li, M. R. Stark, A. D. Johnson, C. Wolberger
Crystal Structure Of The Mata1/Mat Alpha 2 Homeodomain Heterodimer Bound To Dna.
Science V. 270 262 1995
PubMed-ID: 7569974
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*TP*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*TP*AP*TP*TP*AP*C P*AP*TP*CP*A)-3')
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*TP*AP*TP*GP*AP*TP*GP*TP*AP*AP*TP*AP*AP*AP*TP*TP*A P*CP*AP*TP*G)-3')
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - PROTEIN (MAT A1 HOMEODOMAIN)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: MAT A1 RESIDUE 66-126
    Expression System Plasmid: PMS/K66
    Expression System Taxid: 562
    Gene: MAT A1 RESIDUE 66-126
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: T7 PROMOTER
 
Molecule 4 - PROTEIN (MAT ALPHA2 HOMEODOMAIN)
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: MAT ALPHA2 RESIDUE 128-210
    Expression System Plasmid: PAV105
    Expression System Taxid: 562
    Gene: MAT ALPHA2 RESIDUE 128-210
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: TAC PROMOTER

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1YRN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_1PS00027 'Homeobox' domain signature.HMRA1_YEAST103-126  1A:103-125
MATA1_YEASX103-126  1A:103-125

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YCR039C1YCR039C.1III:200174-199542633MTAL2_YEAST1-2102101B:128-20578

(-) 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
(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:49
 aligned with HMRA1_YEAST | P0CY11 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:49
                                    86        96       106       116         
          HMRA1_YEAST    77 ISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS 125
               SCOP domains d1yrna_ A: Mating type protein A1 Homeodomain     SCOP domains
               CATH domains 1yrnA00 A:77-125 Homeodomain-like                 CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------HOMEOBOX_1              PROSITE (2)
                 Transcript ------------------------------------------------- Transcript
                 1yrn A  77 ISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS 125
                                    86        96       106       116         


Chain A from PDB  Type:PROTEIN  Length:49
 aligned with MATA1_YEASX | P0CY10 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:49
                                    86        96       106       116         
          MATA1_YEASX    77 ISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS 125
               SCOP domains d1yrna_ A: Mating type protein A1 Homeodomain     SCOP domains
               CATH domains 1yrnA00 A:77-125 Homeodomain-like                 CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------HOMEOBOX_1              PROSITE
                 Transcript ------------------------------------------------- Transcript
                 1yrn A  77 ISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS 125
                                    86        96       106       116         


Chain B from PDB  Type:PROTEIN  Length:78
 aligned with HMAL2_YEAST | P0CY09 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:78
                                   137       147       157       167       177       187       197        
          HMAL2_YEAST   128 TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTITIAPELADLLSGEPL 205
               SCOP domains d1yrnb_ B: mat alpha2 Homeodomain                                              SCOP domains
               CATH domains 1yrnB00 B:128-205 Homeodomain-like                                             CATH domains
               Pfam domains ---Homeobox-1yrnB01 B:131-189                                 ---------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhh.hhh....hhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 1yrn B 128 TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTITIAPELADLLSGEPL 205
                                   137       147       157       167       177       187       197        


Chain B from PDB  Type:PROTEIN  Length:78
 aligned with MTAL2_YEAST | P0CY08 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:78
                                   137       147       157       167       177       187       197        
          MTAL2_YEAST   128 TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTITIAPELADLLSGEPL 205
               SCOP domains d1yrnb_ B: mat alpha2 Homeodomain                                              SCOP domains
               CATH domains 1yrnB00 B:128-205 Homeodomain-like                                             CATH domains
               Pfam domains ---Homeobox-1yrnB01 B:131-189                                 ---------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhh.hhh....hhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:128-205 UniProt: 1-210 [INCOMPLETE]                           Transcript 1
                 1yrn B 128 TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTITIAPELADLLSGEPL 205
                                   137       147       157       167       177       187       197        


Chain C from PDB  Type:DNA  Length:21
                                                     
                 1yrn C   1 TACATGTAATTTATTACATCA  21
                                    10        20 


Chain D from PDB  Type:DNA  Length:21
                                                     
                 1yrn D  22 TATGATGTAATAAATTACATG  42
                                    31        41
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (12, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HMRA1_YEAST | P0CY11)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003714    transcription corepressor activity    A protein or a member of a complex that interacts specifically and non-covalently with a DNA-bound DNA-binding transcription factor to repress the transcription of specific genes. Corepressors often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second ATP-dependent class modifies the conformation of chromatin. A third class occludes DNA-binding transcription factor protein-protein interaction domains. A third class of corepressors prevents interactions of DNA bound DNA-binding transcription factor with coactivators.
biological process
    GO:1903507    negative regulation of nucleic acid-templated transcription    Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
    GO:0007532    regulation of mating-type specific transcription, DNA-templated    Any mating-type specific process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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: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.

Chain A   (MATA1_YEASX | P0CY10)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    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: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.

Chain B   (HMAL2_YEAST | P0CY09)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008301    DNA binding, bending    The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
    GO:0001227    DNA-binding transcription repressor activity, RNA polymerase II-specific    A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to repress or decrease transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
biological process
    GO:0001198    negative regulation of mating-type specific transcription from RNA polymerase II promoter    Any mating-type specific process that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter.
    GO:0000122    negative regulation of transcription by RNA polymerase II    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II.
    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: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.

Chain B   (MTAL2_YEAST | P0CY08)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008301    DNA binding, bending    The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
    GO:0001227    DNA-binding transcription repressor activity, RNA polymerase II-specific    A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to repress or decrease transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0001198    negative regulation of mating-type specific transcription from RNA polymerase II promoter    Any mating-type specific process that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter.
    GO:0000122    negative regulation of transcription by RNA polymerase II    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II.
    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: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
        HMAL2_YEAST | P0CY09: 1akh 1apl 1k61 1mnm
        HMRA1_YEAST | P0CY11: 1akh 1f43 1le8 1mh3 1mh4
        MATA1_YEASX | P0CY10: 1akh 1f43 1le8 1mh3 1mh4
        MTAL2_YEAST | P0CY08: 1akh 1apl 1k61 1le8 1mnm

(-) Related Entries Specified in the PDB File

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