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(-) Description

Title :  STRUCTURE AND MOBILITY OF THE PUT3 DIMER: A DNA PINCER, NMR, 13 STRUCTURES
 
Authors :  K. J. Walters, K. T. Dayie, R. J. Reece, M. Ptashne, G. Wagner
Date :  12 May 97  (Deposition) - 17 Sep 97  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (13x)
Keywords :  Transcription Regulation, Put3 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Walters, K. T. Dayie, R. J. Reece, M. Ptashne, G. Wagner
Structure And Mobility Of The Put3 Dimer.
Nat. Struct. Biol. V. 4 744 1997
PubMed-ID: 9303003  |  Reference-DOI: 10.1038/NSB0997-744
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUT3
    Chains: A, B
    Fragment: DNA-BINDING DOMAIN, RESIDUES 31 - 100
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: EXPRESSED IN ESCHERICHIA COLI

 Structural Features

(-) Chains, Units

  
NMR Structure (13x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

NMR Structure (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

NMR Structure (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:34 , CYS A:37 , CYS A:44 , CYS A:50 , ZN A:102BINDING SITE FOR RESIDUE ZN A 101
2AC2SOFTWARECYS A:34 , CYS A:50 , CYS A:53 , ILE A:59 , CYS A:60 , ZN A:101BINDING SITE FOR RESIDUE ZN A 102
3AC3SOFTWARECYS B:34 , CYS B:37 , CYS B:44 , CYS B:50 , ZN B:102BINDING SITE FOR RESIDUE ZN B 101
4AC4SOFTWARECYS B:34 , CYS B:50 , CYS B:53 , ILE B:59 , CYS B:60 , ZN B:101BINDING SITE FOR RESIDUE ZN B 102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 26)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13Asn A:48 -Pro A:49
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13Asn B:48 -Pro B:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

NMR Structure (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZN2_CY6_FUNGAL_1PS00463 Zn(2)-C6 fungal-type DNA-binding domain signature.PUT3_YEAST33-60
 		  2A:33-60
B:33-60
2ZN2_CY6_FUNGAL_2PS50048 Zn(2)-C6 fungal-type DNA-binding domain profile.PUT3_YEAST33-62
 		  2A:33-62
B:33-62

(-) Exons   (1, 2)

NMR Structure (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YKL015W1YKL015W.1XI:408187-4111262940PUT3_YEAST1-9799792A:30-100
B:30-100		71
71

(-) Sequences/Alignments

NMR Structure
   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:71
 aligned with PUT3_YEAST | P25502 from UniProtKB/Swiss-Prot  Length:979

    Alignment length:71
                                    39        49        59        69        79        89        99 
           PUT3_YEAST    30 SSVACLSCRKRHIKCPGGNPCQKCVTSNAICEYLEPSKKIVVSTKYLQQLQKDLNDKTEENNRLKALLLER 100
               SCOP domains d1ajya1 A:30-66 PUT3                 d1ajya2 A:67-100 PUT3              SCOP domains
               CATH domains 1ajyA01 A:30-61 CD2-Gal4        --------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .....hhhhh............hhhh.............----hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------eeeee--------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---ZN2_CY6_FUNGAL_1            ---------------------------------------- PROSITE (1)
                PROSITE (2) ---ZN2_CY6_FUNGAL_2  PDB: A:33-62-------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:30-100 UniProt: 1-979 [INCOMPLETE]                     Transcript 1
                 1ajy A  30 MSVACLSCRKRHIKCPGGNPCQKCVTSNAICEYLEPSKKIVVSTKYLQQLQKDLNDKTEENNRLKALLLER 100
                                    39        49        59        69        79        89        99 


Chain B from PDB  Type:PROTEIN  Length:71
 aligned with PUT3_YEAST | P25502 from UniProtKB/Swiss-Prot  Length:979

    Alignment length:71
                                    39        49        59        69        79        89        99 
           PUT3_YEAST    30 SSVACLSCRKRHIKCPGGNPCQKCVTSNAICEYLEPSKKIVVSTKYLQQLQKDLNDKTEENNRLKALLLER 100
               SCOP domains d1ajyb1 B:30-66 PUT3                 d1ajyb2 B:67-100 PUT3              SCOP domains
               CATH domains 1ajyB01 B:30-61 CD2-Gal4        --------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .....hhhhhh...........hhhh.............----hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------eeeee--------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---ZN2_CY6_FUNGAL_1            ---------------------------------------- PROSITE (1)
                PROSITE (2) ---ZN2_CY6_FUNGAL_2  PDB: B:33-62-------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:30-100 UniProt: 1-979 [INCOMPLETE]                     Transcript 1
                 1ajy B  30 MSVACLSCRKRHIKCPGGNPCQKCVTSNAICEYLEPSKKIVVSTKYLQQLQKDLNDKTEENNRLKALLLER 100
                                    39        49        59        69        79        89        99
   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)

NMR Structure
(-)
Class: Coiled coil proteins (689)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

NMR Structure(hide GO term definitions)
Chain A,B   (PUT3_YEAST | P25502)
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:2001158    positive regulation of proline catabolic process to glutamate    Any process that activates or increases the frequency, rate or extent of proline catabolic process to glutamate.
    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:0006560    proline metabolic process    The chemical reactions and pathways involving proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
    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.
    GO:0000972    transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery    The chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery. In S. cerevisiae, this process involves cis-acting DNA sequences such as the TATA box and upstream activating sequence (UAS) elements, trans-acting transcriptional activators, and also the 3'-UTR of the transcript.
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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  1ajy
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  PUT3_YEAST | P25502
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 Related Entries

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        PUT3_YEAST | P25502: 1zme

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