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(-) Description

Title :  STRUCTURE OF A HAP1-18/DNA COMPLEX REVEALS THAT PROTEIN/DNA INTERACTIONS CAN HAVE DIRECT ALLOSTERIC EFFECTS ON TRANSCRIPTIONAL ACTIVATION
 
Authors :  D. A. King, L. Zhang, L. Guarente, R. Marmorstein
Date :  17 Sep 98  (Deposition) - 10 Nov 99  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Complex Transcription Factor-Dna, Asymmetry, Transcriptional Activation, Hyperactive Mutant, Gene Regulation-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. King, L. Zhang, L. Guarente, R. Marmorstein
Structure Of Hap1-18-Dna Implicates Direct Allosteric Effec Of Protein-Dna Interactions On Transcriptional Activation.
Nat. Struct. Biol. V. 6 22 1999
PubMed-ID: 9886287  |  Reference-DOI: 10.1038/4893

(-) Compounds

Molecule 1 - DNA (5'- D(*AP*CP*GP*CP*TP*AP*TP*TP*AP*TP*CP*GP*CP*TP*AP*TP*TP*AP*GP*T)-3')
    Chains: A
    Engineered: YES
    Fragment: UPSTREAM ACTIVATION SEQUENCE
    Other Details: SEQUENCE FROM SACCHAROMYCES CEREVISIAE
    Synonym: UAS CYC7
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*AP*CP*TP*AP*AP*TP*AP*GP*CP*GP*AP*TP*AP*AP*TP*AP*GP*CP*GP*T)-3')
    Chains: B
    Engineered: YES
    Fragment: UPSTREAM ACTIVATION SEQUENCE
    Other Details: SEQUENCE FROM SACCHAROMYCES CEREVISIAE
    Synonym: UAS CYC7
    Synthetic: YES
 
Molecule 3 - PROTEIN (HEME ACTIVATOR PROTEIN)
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (LYSS)
    Expression System Taxid: 562
    Expression System Vector: PRESET-A
    Expression System Vector Type: LAC
    Fragment: DNA-BINDING DOMAIN
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Strain: BWG-1-7A-DCYC1
    Synonym: HAP1.18

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1ZN5Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS C:64 , CYS C:67 , CYS C:74 , CYS C:81 , ZN C:137BINDING SITE FOR RESIDUE ZN C 136
2AC2SOFTWARECYS C:64 , CYS C:81 , CYS C:84 , CYS C:93 , ZN C:136BINDING SITE FOR RESIDUE ZN C 137
3AC3SOFTWAREHIS D:80 , HIS D:91BINDING SITE FOR RESIDUE ZN D 136
4AC4SOFTWARECYS D:64 , CYS D:67 , CYS D:74 , CYS D:81 , ZN D:138BINDING SITE FOR RESIDUE ZN D 137
5AC5SOFTWARECYS D:64 , CYS D:81 , CYS D:84 , CYS D:93 , ZN D:137BINDING SITE FOR RESIDUE ZN D 138
6ZNAUNKNOWNZN C:136 , ZN C:137 , CYS C:64 , CYS C:67 , CYS C:74 , CYS C:81 , CYS C:84 , CYS C:93NULL
7ZNBUNKNOWNZN D:137 , ZN D:138 , CYS D:64 , CYS D:67 , CYS D:74 , CYS D:81 , CYS D:84 , CYS D:93NULL

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HAP)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg C:78 -Pro C:79
2Arg D:78 -Pro D:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HAP)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZN2_CY6_FUNGAL_1PS00463 Zn(2)-C6 fungal-type DNA-binding domain signature.HAP1_YEASK63-93
 		  2C:64-93
D:64-93
HAP1_YEAST63-93
 		  2C:64-93
D:64-93
HAP1_YEASX63-93
 		  2C:64-93
D:64-93
2ZN2_CY6_FUNGAL_2PS50048 Zn(2)-C6 fungal-type DNA-binding domain profile.HAP1_YEASK63-95
 		  2C:64-95
D:64-95
HAP1_YEAST63-95
 		  2C:64-95
D:64-95
HAP1_YEASX63-95
 		  2C:64-95
D:64-95

(-) Exons   (0, 0)

(no "Exon" information available for 2HAP)

(-) 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:20
                                                    
                 2hap A   1 ACGCTATTATCGCTATTAGT  20
                                    10        20


Chain B from PDB  Type:DNA  Length:20
                                                    
                 2hap B   1 ACTAATAGCGATAATAGCGT  20
                                    10        20


Chain C from PDB  Type:PROTEIN  Length:76
 aligned with HAP1_YEASK | G2WJ80 from UniProtKB/Swiss-Prot  Length:1480

    Alignment length:76
                                    64        74        84        94       104       114       124      
           HAP1_YEASK    55 RKRNRIPLSCTICRKRKVKCDKLRPHCQQCTKTGVAHLCHYMEQTWAEEAEKELLKDNELKKLRERVKSLEKTLSK 130
               SCOP domains d2hapc1 C:55-97 Hap1 (Cyp1)                d2hapc2 C:98-130 HAP1             SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh............hhhhhh..hhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------ZN2_CY6_FUNGAL_1  PDB: C:64-93 ------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------ZN2_CY6_FUNGAL_2  PDB: C:64-95   ----------------------------------- PROSITE (3)
                 Transcript ---------------------------------------------------------------------------- Transcript
                 2hap C  55 RKRNRIPLRCTICRKRKVKCDKLRPHCQQCTKTGVAHLCHYMEQTWAEEAEKELLKDNELKKLRERVKSLEKTLSK 130
                                    64        74        84        94       104       114       124      


Chain C from PDB  Type:PROTEIN  Length:76
 aligned with HAP1_YEAST | P0CE41 from UniProtKB/Swiss-Prot  Length:1502

    Alignment length:76
                                    64        74        84        94       104       114       124      
           HAP1_YEAST    55 RKRNRIPLSCTICRKRKVKCDKLRPHCQQCTKTGVAHLCHYMEQTWAEEAEKELLKDNELKKLRERVKSLEKTLSK 130
               SCOP domains d2hapc1 C:55-97 Hap1 (Cyp1)                d2hapc2 C:98-130 HAP1             SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh............hhhhhh..hhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------ZN2_CY6_FUNGAL_2  PDB: C:64-95   ----------------------------------- PROSITE (4)
                PROSITE (5) ---------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) --------ZN2_CY6_FUNGAL_1  PDB: C:64-93 ------------------------------------- PROSITE (6)
                 Transcript ---------------------------------------------------------------------------- Transcript
                 2hap C  55 RKRNRIPLRCTICRKRKVKCDKLRPHCQQCTKTGVAHLCHYMEQTWAEEAEKELLKDNELKKLRERVKSLEKTLSK 130
                                    64        74        84        94       104       114       124      


Chain C from PDB  Type:PROTEIN  Length:76
 aligned with HAP1_YEASX | P0CS82 from UniProtKB/Swiss-Prot  Length:1483

    Alignment length:76
                                    64        74        84        94       104       114       124      
           HAP1_YEASX    55 RKRNRIPLSCTICRKRKVKCDKLRPHCQQCTKTGVAHLCHYMEQTWAEEAEKELLKDNELKKLRERVKSLEKTLSK 130
               SCOP domains d2hapc1 C:55-97 Hap1 (Cyp1)                d2hapc2 C:98-130 HAP1             SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh............hhhhhh..hhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------ZN2_CY6_FUNGAL_2  PDB: C:64-95   ----------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) --------ZN2_CY6_FUNGAL_1  PDB: C:64-93 ------------------------------------- PROSITE (5)
                 Transcript ---------------------------------------------------------------------------- Transcript
                 2hap C  55 RKRNRIPLRCTICRKRKVKCDKLRPHCQQCTKTGVAHLCHYMEQTWAEEAEKELLKDNELKKLRERVKSLEKTLSK 130
                                    64        74        84        94       104       114       124      


Chain D from PDB  Type:PROTEIN  Length:75
 aligned with HAP1_YEASK | G2WJ80 from UniProtKB/Swiss-Prot  Length:1480

    Alignment length:75
                                    65        75        85        95       105       115       125     
           HAP1_YEASK    56 KRNRIPLSCTICRKRKVKCDKLRPHCQQCTKTGVAHLCHYMEQTWAEEAEKELLKDNELKKLRERVKSLEKTLSK 130
               SCOP domains d2hapd1 D:56-97 Hap1 (Cyp1)               d2hapd2 D:98-130 HAP1             SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhh............hhhhhh..hhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------ZN2_CY6_FUNGAL_1  PDB: D:64-93 ------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------ZN2_CY6_FUNGAL_2  PDB: D:64-95   ----------------------------------- PROSITE (3)
                 Transcript --------------------------------------------------------------------------- Transcript
                 2hap D  56 KRNRIPLRCTICRKRKVKCDKLRPHCQQCTKTGVAHLCHYMEQTWAEEAEKELLKDNELKKLRERVKSLEKTLSK 130
                                    65        75        85        95       105       115       125     


Chain D from PDB  Type:PROTEIN  Length:75
 aligned with HAP1_YEAST | P0CE41 from UniProtKB/Swiss-Prot  Length:1502

    Alignment length:75
                                    65        75        85        95       105       115       125     
           HAP1_YEAST    56 KRNRIPLSCTICRKRKVKCDKLRPHCQQCTKTGVAHLCHYMEQTWAEEAEKELLKDNELKKLRERVKSLEKTLSK 130
               SCOP domains d2hapd1 D:56-97 Hap1 (Cyp1)               d2hapd2 D:98-130 HAP1             SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhh............hhhhhh..hhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -------ZN2_CY6_FUNGAL_2  PDB: D:64-95   ----------------------------------- PROSITE (4)
                PROSITE (5) --------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) -------ZN2_CY6_FUNGAL_1  PDB: D:64-93 ------------------------------------- PROSITE (6)
                 Transcript --------------------------------------------------------------------------- Transcript
                 2hap D  56 KRNRIPLRCTICRKRKVKCDKLRPHCQQCTKTGVAHLCHYMEQTWAEEAEKELLKDNELKKLRERVKSLEKTLSK 130
                                    65        75        85        95       105       115       125     


Chain D from PDB  Type:PROTEIN  Length:75
 aligned with HAP1_YEASX | P0CS82 from UniProtKB/Swiss-Prot  Length:1483

    Alignment length:75
                                    65        75        85        95       105       115       125     
           HAP1_YEASX    56 KRNRIPLSCTICRKRKVKCDKLRPHCQQCTKTGVAHLCHYMEQTWAEEAEKELLKDNELKKLRERVKSLEKTLSK 130
               SCOP domains d2hapd1 D:56-97 Hap1 (Cyp1)               d2hapd2 D:98-130 HAP1             SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhh............hhhhhh..hhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------ZN2_CY6_FUNGAL_2  PDB: D:64-95   ----------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) -------ZN2_CY6_FUNGAL_1  PDB: D:64-93 ------------------------------------- PROSITE (5)
                 Transcript --------------------------------------------------------------------------- Transcript
                 2hap D  56 KRNRIPLRCTICRKRKVKCDKLRPHCQQCTKTGVAHLCHYMEQTWAEEAEKELLKDNELKKLRERVKSLEKTLSK 130
                                    65        75        85        95       105       115       125
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Coiled coil proteins (689)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HAP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HAP)

(-) Gene Ontology  (17, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C,D   (HAP1_YEAST | P0CE41)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0000436    carbon catabolite activation of transcription from RNA polymerase II promoter    Any process involving carbon catabolites that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0071169    establishment of protein localization to chromatin    The directed movement of a protein to a part of a chromosome that is organized into chromatin.
    GO:0061428    negative regulation of transcription from RNA polymerase II promoter in response to hypoxia    Any process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
    GO:0043457    regulation of cellular respiration    Any process that modulates the frequency, rate or extent of cellular respiration, the enzymatic release of energy from organic compounds.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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   (HAP1_YEASX | P0CS82)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0043457    regulation of cellular respiration    Any process that modulates the frequency, rate or extent of cellular respiration, the enzymatic release of energy from organic compounds.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates 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   (HAP1_YEASK | G2WJ80)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0043457    regulation of cellular respiration    Any process that modulates the frequency, rate or extent of cellular respiration, the enzymatic release of energy from organic compounds.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates 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
        HAP1_YEASK | G2WJ80: 1hwt 1pyc 1qp9
        HAP1_YEAST | P0CE41: 1hwt 1pyc 1qp9
        HAP1_YEASX | P0CS82: 1hwt 1pyc 1qp9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2HAP)