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(-) Description

Title :  A PARALLEL COILED-COIL TETRAMER WITH OFFSET HELICES
 
Authors :  J. Liu, M. Lu
Date :  12 Oct 06  (Deposition) - 16 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Coiled Coils, Protein Design, Parallel Tetramer, Protein Structure, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Liu, Y. Deng, Q. Zheng, C. S. Cheng, N. R. Kallenbach, M. Lu
A Parallel Coiled-Coil Tetramer With Offset Helices.
Biochemistry V. 45 15224 2006
PubMed-ID: 17176044  |  Reference-DOI: 10.1021/BI061914M

(-) Compounds

Molecule 1 - GENERAL CONTROL PROTEIN GCN4
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PAE4
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: GCN4
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2IPA1Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:18BINDING SITE FOR RESIDUE GOL B 201
2AC2SOFTWAREGLU D:23 , HOH D:315BINDING SITE FOR RESIDUE IPA D 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IPZ)

(-) Exons   (1, 4)

Asymmetric/Biological Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YEL009C1YEL009C.1V:139763-138918846GCN4_YEAST1-2812814A:1-34
B:1-34
C:1-34
D:1-34		34
34
34
34

(-) 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:34
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:34
                                   257       267       277    
           GCN4_YEAST   248 QRMKQLEDKVEELLSKNYHLENEVARLKKLVGER 281
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-34 [INCOMPLETE] Transcript 1
                 2ipz A   1 MKVKQLVDKVEELLSKNYHLVNEVARLVKLVGER  34
                                    10        20        30    


Chain B from PDB  Type:PROTEIN  Length:34
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:34
                                   257       267       277    
           GCN4_YEAST   248 QRMKQLEDKVEELLSKNYHLENEVARLKKLVGER 281
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-34 [INCOMPLETE] Transcript 1
                 2ipz B   1 MKVKQLVDKVEELLSKNYHLVNEVARLVKLVGER  34
                                    10        20        30    


Chain C from PDB  Type:PROTEIN  Length:34
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:34
                                   257       267       277    
           GCN4_YEAST   248 QRMKQLEDKVEELLSKNYHLENEVARLKKLVGER 281
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:1-34 [INCOMPLETE] Transcript 1
                 2ipz C   1 MKVKQLVDKVEELLSKNYHLVNEVARLVKLVGER  34
                                    10        20        30    


Chain D from PDB  Type:PROTEIN  Length:34
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:34
                                   257       267       277    
           GCN4_YEAST   248 QRMKQLEDKVEELLSKNYHLENEVARLKKLVGER 281
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:1-34 [INCOMPLETE] Transcript 1
                 2ipz D   1 MKVKQLVDKVEELLSKNYHLVNEVARLVKLVGER  34
                                    10        20        30
   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 2IPZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (GCN4_YEAST | P03069)
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:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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: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:0001135    transcription factor activity, RNA polymerase II transcription factor recruiting    The function of binding to an RNA polymerase II (RNAP II) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP II.
    GO:0001084    transcription factor activity, TFIID-class binding    Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0001190    transcriptional activator activity, RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
    GO:0001191    transcriptional repressor activity, RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
biological process
    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:0010691    negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to nutrient levels    Any process that decreases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter, as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
    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:0001080    nitrogen catabolite activation of transcription from RNA polymerase II promoter    A transcription regulation process in which the presence of one nitrogen source leads to an increase in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.
    GO:0045899    positive regulation of RNA polymerase II transcriptional preinitiation complex assembly    Any process that activates or increases the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
    GO:1903833    positive regulation of cellular response to amino acid starvation    Any process that activates or increases the frequency, rate or extent of cellular response to amino acid starvation.
    GO:0060261    positive regulation of transcription initiation from RNA polymerase II promoter    Any process that increases the rate, frequency or extent of a process involved in starting 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:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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.
    GO:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GCN4_YEAST | P03069: 1ce9 1dgc 1env 1fav 1fmh 1gcl 1gcm 1gk6 1gzl 1ihq 1ij0 1ij1 1ij2 1ij3 1kql 1ld4 1llm 1nkn 1piq 1rb4 1rb5 1rb6 1swi 1tmz 1unt 1unu 1unv 1unw 1unx 1uny 1unz 1uo0 1uo1 1uo2 1uo3 1uo4 1uo5 1w5g 1w5h 1w5i 1w5j 1w5k 1w5l 1ysa 1zii 1zij 1zik 1zil 1zim 1zta 2ahp 2b1f 2b22 2bni 2cce 2ccf 2ccn 2d3e 2dgc 2efr 2efs 2g9j 2hy6 2k8x 2lpb 2n9b 2nrn 2o7h 2ovn 2vky 2vnl 2wg5 2wg6 2wpy 2wpz 2wq0 2wq1 2wq2 2wq3 2yny 2ynz 2yo0 2yo1 2yo2 2yo3 2z5h 2z5i 2zta 3azd 3bas 3bat 3ck4 3crp 3g9r 3gjp 3i1g 3i5c 3k7z 3m48 3p8m 3zmf 4c46 4dmd 4g2k 4hu5 4hu6 4niz 4nj0 4nj1 4nj2 4owi 4tl1 5app 5apq 5aps 5apt 5apu 5apv 5apw 5apx 5apy 5apz 5iew 5iir 5iiv 5kht

(-) Related Entries Specified in the PDB File

2b1f MUTANT OF 2ZTA
2b22 MUTANT OF 2ZTA
2hy6 MUTANT OF 2ZTA
2zta