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(-) Description

Title :  CRYSTAL STRUCTURE OF A MAT-ALPHA2 HOMEODOMAIN-OPERATOR COMPLEX SUGGESTS A GENERAL MODEL FOR HOMEODOMAIN-DNA INTERACTIONS
 
Authors :  C. Wolberger, A. K. Vershon, B. Liu, A. D. Johnson, C. O. Pabo
Date :  04 Oct 93  (Deposition) - 21 Oct 93  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Dna Complex, Double Helix, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Wolberger, A. K. Vershon, B. Liu, A. D. Johnson, C. O. Pabo
Crystal Structure Of A Mat Alpha 2 Homeodomain-Operator Complex Suggests A General Model For Homeodomain-Dna Interactions.
Cell(Cambridge, Mass. ) V. 67 517 1991
PubMed-ID: 1682054  |  Reference-DOI: 10.1016/0092-8674(91)90526-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*CP*AP*TP*TP*TP*AP*C P*AP*CP*GP*C)-3')
    Chains: A
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*TP*GP*CP*GP*TP*GP*TP*AP*AP*AP*TP*GP*AP*AP*TP*TP*A P*CP*AP*TP*G)-3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - PROTEIN (MAT-ALPHA2 HOMEODOMAIN)
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: MAT ALPHA2 RES. 128-210
    Expression System Plasmid: PAV56
    Expression System Taxid: 562
    Gene: MAT ALPHA2 RES. 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 1APL)

(-) Sites  (0, 0)

(no "Site" information available for 1APL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YCR039C1YCR039C.1III:200174-199542633MTAL2_YEAST1-2102102C:131-189
D:132-189		59
58

(-) 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:DNA  Length:21
                                                     
                 1apl A   1 ACATGTAATTCATTTACACGC  21
                                    10        20 


Chain B from PDB  Type:DNA  Length:21
                                                     
                 1apl B  22 TGCGTGTAAATGAATTACATG  42
                                    31        41 


Chain C from PDB  Type:PROTEIN  Length:59
 aligned with HMAL2_YEAST | P0CY09 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:59
                                   140       150       160       170       180         
          HMAL2_YEAST   131 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 189
               SCOP domains d1aplc_ C: mat alpha2 Homeodomain                           SCOP domains
               CATH domains 1aplC00 C:131-189 Homeodomain-like                          CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 1apl C 131 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 189
                                   140       150       160       170       180         


Chain C from PDB  Type:PROTEIN  Length:59
 aligned with MTAL2_YEAST | P0CY08 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:59
                                   140       150       160       170       180         
          MTAL2_YEAST   131 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 189
               SCOP domains d1aplc_ C: mat alpha2 Homeodomain                           SCOP domains
               CATH domains 1aplC00 C:131-189 Homeodomain-like                          CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:131-189 UniProt: 1-210 [INCOMPLETE]        Transcript 1
                 1apl C 131 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 189
                                   140       150       160       170       180         


Chain D from PDB  Type:PROTEIN  Length:58
 aligned with HMAL2_YEAST | P0CY09 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:58
                                   141       151       161       171       181        
          HMAL2_YEAST   132 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 189
               SCOP domains d1apld_ D: mat alpha2 Homeodomain                          SCOP domains
               CATH domains 1aplD00 D:132-189 Homeodomain-like                         CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 1apl D 132 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 189
                                   141       151       161       171       181        


Chain D from PDB  Type:PROTEIN  Length:58
 aligned with MTAL2_YEAST | P0CY08 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:58
                                   141       151       161       171       181        
          MTAL2_YEAST   132 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 189
               SCOP domains d1apld_ D: mat alpha2 Homeodomain                          SCOP domains
               CATH domains 1aplD00 D:132-189 Homeodomain-like                         CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:132-189 UniProt: 1-210 [INCOMPLETE]       Transcript 1
                 1apl D 132 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 189
                                   141       151       161       171       181
   Legend:   → Mismatch (orange background)
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  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/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 1APL)

(-) Gene Ontology  (9, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C,D   (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 C,D   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        HMAL2_YEAST | P0CY09: 1akh 1k61 1mnm 1yrn
        MTAL2_YEAST | P0CY08: 1akh 1k61 1le8 1mnm 1yrn

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