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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MATA1/MATALPHA2-3A HETERODIMER BOUND TO DNA COMPLEX
 
Authors :  A. Ke, J. R. Mathias, A. K. Vershon, C. Wolberger
Date :  09 Apr 02  (Deposition) - 03 May 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Matalpha2, Isothermal Titration Calorimetry, Protein-Dna Complex, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ke, J. R. Mathias, A. K. Vershon, C. Wolberger
Structural And Thermodynamic Characterization Of The Dna Binding Properties Of A Triple Alanine Mutant Of Matalpha2
Structure V. 10 961 2002
PubMed-ID: 12121651  |  Reference-DOI: 10.1016/S0969-2126(02)00790-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*AP*CP*AP*TP*GP*TP*AP*AP*AP*AP*AP*TP*TP*TP*AP*CP*AP*TP*CP *A)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'- D(*TP*TP*GP*AP*TP*GP*TP*AP*AP*AP*TP*TP*TP*TP*TP*AP*CP*AP*TP *G)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - MATING-TYPE PROTEIN A-1
    Chains: A
    Engineered: YES
    Fragment: RESIDUES 74-126
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED WITH SOLID PHASE PEPTIDE SYNTHESIZER. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN SACCHAROMYCES CEREVISIAE (YEAST).
    Synonym: MAT A1
    Synthetic: YES
 
Molecule 4 - MATING-TYPE PROTEIN ALPHA-2
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PAK2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 128-210
    Gene: MATALPHA2
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: MAT ALPHA2, ALPHA-2 REPRESSOR

 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 1LE8)

(-) Sites  (0, 0)

(no "Site" information available for 1LE8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LE8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LE8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LE8)

(-) PROSITE Motifs  (1, 1)

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

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YCR039C1YCR039C.1III:200174-199542633MTAL2_YEAST1-2102101B:132-20574

(-) 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:53
 aligned with HMRA1_YEAST | P0CY11 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:53
                                    83        93       103       113       123   
          HMRA1_YEAST    74 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 126
               SCOP domains d1le8a_ A: Mating type protein A1 Homeodomain         SCOP domains
               CATH domains 1le8A00 A:74-126 Homeodomain-like                     CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------HOMEOBOX_1               PROSITE (2)
                 Transcript ----------------------------------------------------- Transcript
                 1le8 A  74 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 126
                                    83        93       103       113       123   


Chain A from PDB  Type:PROTEIN  Length:53
 aligned with MATA1_YEASX | P0CY10 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:53
                                    83        93       103       113       123   
          MATA1_YEASX    74 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 126
               SCOP domains d1le8a_ A: Mating type protein A1 Homeodomain         SCOP domains
               CATH domains 1le8A00 A:74-126 Homeodomain-like                     CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------HOMEOBOX_1               PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 1le8 A  74 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 126
                                    83        93       103       113       123   


Chain B from PDB  Type:PROTEIN  Length:74
 aligned with HMRA2_YEAST | P0CY13 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:74
                                    50        60        70        80        90       100       110    
          HMRA2_YEAST    41 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTITIAPELADLLSGEPL 114
               SCOP domains d1le8b_ B: mat alpha2 Homeodomain                                          SCOP domains
               CATH domains 1le8B00 B:132-205 Homeodomain-like                                         CATH domains
               Pfam domains Homeobox-1le8B01 B:132-189                                ---------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 1le8 B 132 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITIAPELADLLSGEPL 205
                                   141       151       161       171       181       191       201    


Chain B from PDB  Type:PROTEIN  Length:74
 aligned with MATA2_YEASX | P0CY12 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:74
                                    50        60        70        80        90       100       110    
          MATA2_YEASX    41 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTITIAPELADLLSGEPL 114
               SCOP domains d1le8b_ B: mat alpha2 Homeodomain                                          SCOP domains
               CATH domains 1le8B00 B:132-205 Homeodomain-like                                         CATH domains
               Pfam domains Homeobox-1le8B01 B:132-189                                ---------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 1le8 B 132 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITIAPELADLLSGEPL 205
                                   141       151       161       171       181       191       201    


Chain B from PDB  Type:PROTEIN  Length:74
 aligned with MTAL2_YEAST | P0CY08 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:74
                                   141       151       161       171       181       191       201    
          MTAL2_YEAST   132 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTITIAPELADLLSGEPL 205
               SCOP domains d1le8b_ B: mat alpha2 Homeodomain                                          SCOP domains
               CATH domains 1le8B00 B:132-205 Homeodomain-like                                         CATH domains
               Pfam domains Homeobox-1le8B01 B:132-189                                ---------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:132-205 UniProt: 1-210 [INCOMPLETE]                       Transcript 1
                 1le8 B 132 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITIAPELADLLSGEPL 205
                                   141       151       161       171       181       191       201    


Chain C from PDB  Type:DNA  Length:20
                                                    
                 1le8 C   2 ACATGTAAAAATTTACATCA  21
                                    11        21


Chain D from PDB  Type:DNA  Length:20
                                                    
                 1le8 D  23 TTGATGTAAATTTTTACATG  42
                                    32        42
   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  (14, 28)

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   (HMRA2_YEAST | P0CY13)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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.

Chain B   (MATA2_YEASX | P0CY12)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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
        HMRA1_YEAST | P0CY11: 1akh 1f43 1mh3 1mh4 1yrn
        HMRA2_YEAST | P0CY13: 1k61
        MATA1_YEASX | P0CY10: 1akh 1f43 1mh3 1mh4 1yrn
        MATA2_YEASX | P0CY12: 1k61
        MTAL2_YEAST | P0CY08: 1akh 1apl 1k61 1mnm 1yrn

(-) Related Entries Specified in the PDB File

1akh VARIANT MATA1MATALPHA2 DNA TERNARY COMPLEX
1yrn MAT A1/ALPHA2/DNA TERNARY COMPLEX (HOMEODOMAIN)