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(-) Description

Title :  STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
 
Authors :  M. K. Yadav, J. E. Redman, J. M. Alvarez-Gutierrez, Y. Zhang, C. D. Stout, M. R. Ghadiri
Date :  15 Sep 03  (Deposition) - 13 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Four Helix Bundle, Cavity (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. K. Yadav, J. E. Redman, L. J. Leman, J. M. Alvarez-Gutierrez, Y. Zhang, C. D. Stout, M. R. Ghadiri
Structure-Based Engineering Of Internal Cavities In Coiled-Coil Peptides
Biochemistry V. 44 9723 2005
PubMed-ID: 16008357  |  Reference-DOI: 10.1021/BI050742A

(-) Compounds

Molecule 1 - GENERAL CONTROL PROTEIN GCN4
    ChainsA, B
    MutationYES
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    Other DetailsDIMER ASYMMETRIC UNIT OF FOUR HELIX BUNDLE MUTATION LEU26ALA
    Other Details - SourceBASED ON SEQUENCE FROM SACCHAROMYCES CEREVISIAE (BAKER'S YEAST)
    SynonymGCN4 LEUCINE ZIPPER, AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN, PLI
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1UO0)

(-) Sites  (0, 0)

(no "Site" information available for 1UO0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UO0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UO0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UO0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UO0)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YEL009C1YEL009C.1V:139763-138918846GCN4_YEAST1-2812812A:1-32
B:1-32
32
32

(-) Sequences/Alignments

Asymmetric 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:32
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:32
                                   258       268       278  
           GCN4_YEAST   249 RMKQLEDKVEELLSKNYHLENEVARLKKLVGE 280
               SCOP domains d1uo0a_ A: GCN4                  SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-32            Transcript 1
                 1uo0 A   1 RMKQIEDKLEEILSKLYHIENELARAKKLLGE  32
                                    10        20        30  

Chain B from PDB  Type:PROTEIN  Length:32
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:32
                                   258       268       278  
           GCN4_YEAST   249 RMKQLEDKVEELLSKNYHLENEVARLKKLVGE 280
               SCOP domains d1uo0b_ B: GCN4                  SCOP domains
               CATH domains -------------------------------- CATH domains
           Pfam domains (1) bZIP_1-1uo0B01 B:1-32            Pfam domains (1)
           Pfam domains (2) bZIP_1-1uo0B02 B:1-32            Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-32            Transcript 1
                 1uo0 B   1 RMKQIEDKLEEILSKLYHIENELARAKKLLGE  32
                                    10        20        30  

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  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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1UO0)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: bZIP (54)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 | P030691ce9 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 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 2ipz 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

1ce9 HELIX CAPPING IN THE GCN4 LEUCINE ZIPPER
1dgc GCN4 LEUCINE ZIPPER COMPLEXED WITH SPECIFIC ATF/CREB SITE DEOXYRIBONUCLEIC ACID
1env ATOMIC STRUCTURE OF THE ECTODOMAIN FROM HIV -1 GP41
1fav THE STRUCTURE OF AN HIV-1 SPECIFIC CELL ENTRY INHIBITOR INCOMPLEX WITH THE HIV-1 GP41 TRIMERIC CORE
1gcl GCN4 LEUCINE ZIPPER CORE MUTANT P-LI
1gcm GCN4 LEUCINE ZIPPER CORE MUTANT P-LI
1gk6 HUMAN VIMENTIN COIL 2B FRAGMENT LINKED TO GCN4 LEUCINE ZIPPER (Z2B)
1gzl CRYSTAL STRUCTURE OF C14LINKMID/IQN17: A CROSS-LINKED INHIBITOR OF HIV-1 ENTRY BOUND TO THE GP41 HYDROPHOBIC POCKET
1ihq GLYTM1BZIP: A CHIMERIC PEPTIDE MODEL OF THE N-TERMINUS OF ARAT SHORT ALPHA TROPOMYOSIN WITH THE N-TERMINUS ENCODED BYEXON 1B
1ij0 COILED COIL TRIMER GCN4-PVLS SER AT BURIED D POSITION
1ij1 GCN4-PVLT COILED-COIL TRIMER WITH THREONINE AT THE D(12)POSITION
1ij2 GCN4-PVTL COILED-COIL TRIMER WITH THREONINE AT THE A(16)POSITION
1ij3 GCN4-PVSL COILED-COIL TRIMER WITH SERINE AT THE A(16)POSITION
1kql CRYSTAL STRUCTURE OF THE C-TERMINAL REGION OF STRIATEDMUSCLE ALPHA-TROPOMYOSIN AT 2.7 ANGSTROM RESOLUTION
1ld4 PLACEMENT OF THE STRUCTURAL PROTEINS IN SINDBIS VIRUS
1llm CRYSTAL STRUCTURE OF A ZIF23-GCN4 CHIMERA BOUND TO DNA
1nkn VISUALIZING AN UNSTABLE COILED COIL: THE CRYSTAL STRUCTUREOF AN N-TERMINAL SEGMENT OF THE SCALLOP MYOSIN ROD
1piq CRYSTAL STRUCTURE OF GCN4-PIQ, A TRIMERIC COILED COIL WITH BURIED POLAR RESIDUES
1rb1 GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A TRIGONAL AUTOMATICSOLUTION
1rb4 ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT ASN16A TETRAGONAL AUTOMATIC SOLUTION
1rb5 ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT ASN16A TRIGONAL FORM
1rb6 ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT ASN16A TETRAGONAL FORM
1swi GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A COMPLEXED WITH BENZENE
1tmz TMZIP: A CHIMERIC PEPTIDE MODEL OF THE N- TERMINUS OF ALPHA TROPOMYOSIN, NMR, 15 STRUCTURES
1unt STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1unu STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1unv STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1unw STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1unx STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1uny STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1unz STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1uo1 STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1uo2 STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1uo3 STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1uo4 STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1uo5 STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1w5g AN ANTI-PARALLEL FOUR HELIX BUNDLE ( ACETIMIDE MODIFICATION).
1w5h AN ANTI-PARALLEL FOUR HELIX BUNDLE.
1w5i ABA DOES NOT AFFECT TOPOLOGY OF PLI.
1w5j AN ANTI-PARALLEL FOUR HELIX BUNDLE
1w5k AN ANTI-PARALLEL FOUR HELIX BUNDLE
1w5l AN ANTI-PARALLEL TO PARALLEL SWITCH.
1ysa GCN4 (BASIC REGION, LEUCINE ZIPPER) COMPLEX WITH AP-1 DEOXYRIBONUCLEIC ACID
1zii GCN4-LEUCINE ZIPPER CORE MUTANT ASN16ABA IN THE DIMERIC STATE
1zij GCN4-LEUCINE ZIPPER CORE MUTANT ASN16ABA IN THE TRIMERIC STATE
1zik GCN4-LEUCINE ZIPPER CORE MUTANT ASN16LYS IN THE DIMERIC STATE
1zil GCN4-LEUCINE ZIPPER CORE MUTANT ASN16GLN IN THE DIMERIC STATE
1zim GCN4-LEUCINE ZIPPER CORE MUTANT ASN16GLN IN THE TRIMERIC STATE
1zta LEUCINE ZIPPER MONOMER (NMR, 20 STRUCTURES)
2dgc GCN4 BASIC DOMAIN, LEUCINE ZIPPER COMPLEXED WITH ATF/CREB SITE DEOXYRIBONUCLEIC ACID
2zta GCN4 LEUCINE ZIPPER