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(-) Description

Title :  CRYSTAL STRUCTURE OF A LEU3 DNA-BINDING DOMAIN COMPLEXED WITH A 15MER DNA DUPLEX
 
Authors :  M. X. Fitzgerald, R. Marmorstein
Date :  24 Oct 05  (Deposition) - 04 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Zn(2)Cys(6)Binuclear Cluster Motif, Transcription Activator/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. X. Fitzgerald, J. R. Rojas, J. M. Kim, G. B. Kohlhaw, R. Marmorstein
Structure Of A Leu3-Dna Complex: Recognition Of Everted Cgg Half-Sites By A Zn2Cys6 Binuclear Cluster Protein.
Structure V. 14 725 2006
PubMed-ID: 16615914  |  Reference-DOI: 10.1016/J.STR.2005.11.025
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*TP*TP*GP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*CP*A)-3'
    Chains: C, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - REGULATORY PROTEIN LEU3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 32-103
    Gene: LEU3
    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  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:37 , CYS A:57 , CYS A:60 , CYS A:67 , ZN A:105BINDING SITE FOR RESIDUE ZN A 104
2AC2SOFTWARECYS A:37 , CYS A:40 , CYS A:47 , CYS A:57 , ZN A:104BINDING SITE FOR RESIDUE ZN A 105
3AC3SOFTWARECYS B:37 , CYS B:57 , CYS B:60 , CYS B:67 , ZN B:105BINDING SITE FOR RESIDUE ZN B 104
4AC4SOFTWARECYS B:37 , CYS B:40 , CYS B:47 , CYS B:57 , ZN B:104BINDING SITE FOR RESIDUE ZN B 105

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ERE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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.LEUR_YEAST36-67
 		  2A:36-67
B:36-67
2ZN2_CY6_FUNGAL_2PS50048 Zn(2)-C6 fungal-type DNA-binding domain profile.LEUR_YEAST36-69
 		  2A:36-69
B:36-69

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR451W1YLR451W.1XII:1036090-10387502661LEUR_YEAST1-8868862A:35-99 (gaps)
B:35-99 (gaps)		65
65

(-) 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:60
 aligned with LEUR_YEAST | P08638 from UniProtKB/Swiss-Prot  Length:886

    Alignment length:65
                                    44        54        64        74        84        94     
            LEUR_YEAST   35 FACVECRQQKSKCDAHERAPEPCTKCAKKNVPCILKRDFRRTYKRARNEAIEKRFKELTRTLTNL 99
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh......-----..hhhhhh.............hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ZN2_CY6_FUNGAL_1  PDB: A:36-67  -------------------------------- PROSITE (1)
                PROSITE (2) -ZN2_CY6_FUNGAL_2  PDB: A:36-69    ------------------------------ PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:35-99 (gaps) UniProt: 1-886 [INCOMPLETE]         Transcript 1
                  2ere A 35 FACVECRQQKSKCDAH-----PCTKCAKKNVPCILKRDFRRTYKRARNEAIEKRFKELTRTLTNL 99
                                    44     |   - |      64        74        84        94     
                                          50    56                                           


Chain B from PDB  Type:PROTEIN  Length:60
 aligned with LEUR_YEAST | P08638 from UniProtKB/Swiss-Prot  Length:886

    Alignment length:65
                                    44        54        64        74        84        94     
            LEUR_YEAST   35 FACVECRQQKSKCDAHERAPEPCTKCAKKNVPCILKRDFRRTYKRARNEAIEKRFKELTRTLTNL 99
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh......-----..hhhhhh.............hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ZN2_CY6_FUNGAL_1  PDB: B:36-67  -------------------------------- PROSITE (1)
                PROSITE (2) -ZN2_CY6_FUNGAL_2  PDB: B:36-69    ------------------------------ PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:35-99 (gaps) UniProt: 1-886 [INCOMPLETE]         Transcript 1
                  2ere B 35 FACVECRQQKSKCDAH-----PCTKCAKKNVPCILKRDFRRTYKRARNEAIEKRFKELTRTLTNL 99
                                    44     |   - |      64        74        84        94     
                                          50    56                                           


Chain C from PDB  Type:DNA  Length:15
                                              
                  2ere C  1 TTGCCGGTACCGGCA 15
                                    10     


Chain D from PDB  Type:DNA  Length:15
                                              
                  2ere D 16 TTGCCGGTACCGGCA 30
                                    25
   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  (0, 0)

(no "SCOP Domain" information available for 2ERE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LEUR_YEAST | P08638)
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: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:0001078    transcriptional repressor 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 stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009082    branched-chain amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009098    leucine biosynthetic process    The chemical reactions and pathways resulting in the formation of leucine, 2-amino-4-methylpentanoic acid.
    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:2001278    positive regulation of leucine biosynthetic process    Any process that activates or increases the frequency, rate or extent of leucine biosynthetic process.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases 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: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: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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  2ere
    Family and Domain Information: ProDom | SYSTERS
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  LEUR_YEAST | P08638
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 Related Entries

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

UniProtKB/Swiss-Prot
        LEUR_YEAST | P08638: 2er8 2erg

(-) Related Entries Specified in the PDB File

2er8 2erg