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(-) Description

Title :  MAT A1/ALPHA2/DNA TERNARY COMPLEX
 
Authors :  T. Li, Y. Jin, A. K. Vershon, C. Wolberger
Date :  19 May 97  (Deposition) - 20 May 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Complex (Two Dna-Binding Proteins/Dna), Complex, Dna- Binding Protein, Dna, Transcription Regulation, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Li, Y. Jin, A. K. Vershon, C. Wolberger
Crystal Structure Of The Mata1/Matalpha2 Homeodomain Heterodimer In Complex With Dna Containing An A-Tract.
Nucleic Acids Res. V. 26 5707 1998
PubMed-ID: 9838003  |  Reference-DOI: 10.1093/NAR/26.24.5707
(for further references see the PDB file header)

(-) Compounds

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

 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 1AKH)

(-) Sites  (0, 0)

(no "Site" information available for 1AKH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 d1akha_ A: Mating type protein A1 Homeodomain     SCOP domains
               CATH domains 1akhA00 A:77-125 Homeodomain-like                 CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------HOMEOBOX_1              PROSITE
                 Transcript ------------------------------------------------- Transcript
                 1akh A  77 ISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS 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 d1akha_ A: Mating type protein A1 Homeodomain     SCOP domains
               CATH domains 1akhA00 A:77-125 Homeodomain-like                 CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------HOMEOBOX_1              PROSITE (2)
                 Transcript ------------------------------------------------- Transcript
                 1akh A  77 ISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS 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 d1akhb_ B: mat alpha2 Homeodomain                                              SCOP domains
               CATH domains 1akhB00 B:128-205 Homeodomain-like                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 1akh 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 d1akhb_ B: mat alpha2 Homeodomain                                              SCOP domains
               CATH domains 1akhB00 B:128-205 Homeodomain-like                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:128-205 UniProt: 1-210 [INCOMPLETE]                           Transcript 1
                 1akh B 128 TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTITIAPELADLLSGEPL 205
                                   137       147       157       167       177       187       197        


Chain C from PDB  Type:DNA  Length:21
                                                     
                 1akh C   1 TACATGTAAAAATTTACATCA  21
                                    10        20 


Chain D from PDB  Type:DNA  Length:21
                                                     
                 1akh D  22 TATGATGTAAATTTTTACATG  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  (0, 0)

(no "Pfam Domain" information available for 1AKH)

(-) 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    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
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    transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in the regulatory region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
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 from RNA polymerase II promoter    Any process that stops, prevents, or reduces 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: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: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:0001227    transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in the regulatory region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
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 from RNA polymerase II promoter    Any process that stops, prevents, or reduces 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: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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  1akh
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 Related Entries

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

UniProtKB/Swiss-Prot
        HMAL2_YEAST | P0CY09: 1apl 1k61 1mnm 1yrn
        HMRA1_YEAST | P0CY11: 1f43 1le8 1mh3 1mh4 1yrn
        MATA1_YEASX | P0CY10: 1f43 1le8 1mh3 1mh4 1yrn
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(-) Related Entries Specified in the PDB File

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