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(-) Description

Title :  CRYSTAL STRUCTURE OF PUT3/DNA COMPLEX
 
Authors :  K. Swaminathan, R. Marmorstein
Date :  06 Aug 97  (Deposition) - 16 Sep 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Complex (Transcription Regulation/Dna), Put3, Zn2Cys6, Binuclear Cluster, Transcription Factor, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Swaminathan, P. Flynn, R. J. Reece, R. Marmorstein
Crystal Structure Of A Put3-Dna Complex Reveals A Novel Mechanism For Dna Recognition By A Protein Containing A Zn2Cys6 Binuclear Cluster.
Nat. Struct. Biol. V. 4 751 1997
PubMed-ID: 9303004  |  Reference-DOI: 10.1038/NSB0997-751
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*AP*CP*GP*GP*GP*AP*AP*GP*CP*CP*AP*AP*CP*TP*CP*CP*G)-3')
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: PUT3 (31-100)
    Expression System Strain: BL21 (DE3) LYS-S
    Expression System Taxid: 562
    Expression System Vector: PET16B
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
 
Molecule 2 - DNA (5'-D(*AP*CP*GP*GP*AP*GP*(5IU) P*TP*GP*GP*CP*TP*(5IU)P*CP*CP*CP*G)-3')
    Chains: B
    Engineered: YES
 
Molecule 3 - PROLINE UTILIZATION TRANSCRIPTION ACTIVATOR
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 31 - 100
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: PUT3 (PROLINE UTILIZATION TRANSCRIPTION ACTIVATOR)

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
15IU2Mod. Nucleotide5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREZN C:2 , CYS C:34 , CYS C:37 , CYS C:44 , CYS C:50BINDING SITE FOR RESIDUE ZN C 1
2AC2SOFTWAREZN C:1 , CYS C:34 , CYS C:50 , CYS C:53 , CYS C:60BINDING SITE FOR RESIDUE ZN C 2
3AC3SOFTWAREZN D:2 , CYS D:34 , CYS D:37 , CYS D:44 , CYS D:50BINDING SITE FOR RESIDUE ZN D 1
4AC4SOFTWAREZN D:1 , CYS D:34 , CYS D:50 , CYS D:53 , CYS D:60BINDING SITE FOR RESIDUE ZN D 2

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn C:48 -Pro C:49
2Asn D:48 -Pro D:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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.PUT3_YEAST33-60
 		  2C:33-60
D:33-60
2ZN2_CY6_FUNGAL_2PS50048 Zn(2)-C6 fungal-type DNA-binding domain profile.PUT3_YEAST33-62
 		  2C:33-62
D:33-62

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YKL015W1YKL015W.1XI:408187-4111262940PUT3_YEAST1-9799792C:31-100
D:31-100		70
70

(-) 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:17
                                                 
                 1zme A   1 ACGGGAAGCCAACTCCG  17
                                    10       


Chain B from PDB  Type:DNA  Length:17
                                                 
                 1zme B   1 ACGGAGuTGGCTuCCCG  17
                                  | 10  |    
                                  7-5IU |    
                                       13-5IU


Chain C from PDB  Type:PROTEIN  Length:70
 aligned with PUT3_YEAST | P25502 from UniProtKB/Swiss-Prot  Length:979

    Alignment length:70
                                    40        50        60        70        80        90       100
           PUT3_YEAST    31 SVACLSCRKRHIKCPGGNPCQKCVTSNAICEYLEPSKKIVVSTKYLQQLQKDLNDKTEENNRLKALLLER 100
               SCOP domains d1zmec1 C:31-66 PUT3                d1zmec2 C:67-100 PUT3              SCOP domains
               CATH domains 1zmeC01 C:31-61 CD2-Gal4       --------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh...........................eeeeehhhhhhh..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --ZN2_CY6_FUNGAL_1            ---------------------------------------- PROSITE (1)
                PROSITE (2) --ZN2_CY6_FUNGAL_2  PDB: C:33-62-------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: C:31-100 UniProt: 1-979 [INCOMPLETE]                    Transcript 1
                 1zme C  31 SVACLSCRKRHIKCPGGNPCQKCVTSNAICEYLEPSKKIVVSTKYLQQLQKDLNDKTEENNRLKALLLER 100
                                    40        50        60        70        80        90       100


Chain D from PDB  Type:PROTEIN  Length:70
 aligned with PUT3_YEAST | P25502 from UniProtKB/Swiss-Prot  Length:979

    Alignment length:70
                                    40        50        60        70        80        90       100
           PUT3_YEAST    31 SVACLSCRKRHIKCPGGNPCQKCVTSNAICEYLEPSKKIVVSTKYLQQLQKDLNDKTEENNRLKALLLER 100
               SCOP domains d1zmed1 D:31-66 PUT3                d1zmed2 D:67-100 PUT3              SCOP domains
               CATH domains 1zmeD01 D:31-61 CD2-Gal4       --------------------------------------- CATH domains
           Pfam domains (1) -Zn_clus-1zmeD01 D:32-69               ------------------------------- Pfam domains (1)
           Pfam domains (2) -Zn_clus-1zmeD02 D:32-69               ------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhhh.............hhh...........eeeeehhhhhhh..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --ZN2_CY6_FUNGAL_1            ---------------------------------------- PROSITE (1)
                PROSITE (2) --ZN2_CY6_FUNGAL_2  PDB: D:33-62-------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: D:31-100 UniProt: 1-979 [INCOMPLETE]                    Transcript 1
                 1zme D  31 SVACLSCRKRHIKCPGGNPCQKCVTSNAICEYLEPSKKIVVSTKYLQQLQKDLNDKTEENNRLKALLLER 100
                                    40        50        60        70        80        90       100
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Zn_clus] (4)

(-) Gene Ontology  (14, 14)

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

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        PUT3_YEAST | P25502: 1ajy

(-) Related Entries Specified in the PDB File

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