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(-) Description

Title :  STRUCTURE OF THE GCM DOMAIN BOUND TO DNA
 
Authors :  S. X. Cohen, C. W. Muller
Date :  19 Feb 03  (Deposition) - 08 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Transcription Factor/Dna, Transcription Factor, Dna-Binding Domain, Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. X. Cohen, M. Moulin, S. Hashemolhosseini, K. Kilian, M. Wegner, C. W. Muller
Crystal Structure Of The Gcm Domain-Dna Complex: A Dna-Binding Domain With A Novel Fold And Mode Of Target Site Recognition
Embo J. V. 22 1835 2003
PubMed-ID: 12682016  |  Reference-DOI: 10.1093/EMBOJ/CDG182

(-) Compounds

Molecule 1 - MGCM1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: GCM DOMAIN, RESIDUES 1-174
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: ZN-CONTAINING DNA-BINDING DOMAIN
    Synonym: MURINE GCMA (GLIA CELL MISSING) TRANSCRIPTION FACTOR GCM1
 
Molecule 2 - 5'-D(*CP*GP*AP*TP*GP*CP*GP*GP*GP*TP *GP*CP*A)-3'
    Chains: C
    Other Details: DNA TARGET SITE OF THE GCM DOMAIN
    Synonym: DNA OLIGONUCLEOTIDE
    Synthetic: YES
 
Molecule 3 - 5'-D(*TP*GP*CP*AP*CP*CP*CP*GP*CP*AP *TP*CP*G)-3'
    Chains: D
    Other Details: DNA TARGET SITE OF THE GCM DOMAIN
    Synonym: DNA OLIGONUCLEOTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:76 , CYS A:125 , HIS A:152 , HIS A:154BINDING SITE FOR RESIDUE ZN A1171
2AC2SOFTWARECYS A:82 , CYS A:86 , CYS A:113 , CYS A:116BINDING SITE FOR RESIDUE ZN A1172

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GCMPS50807 GCM domain profile.GCM1_MOUSE14-169  1A:14-169

(-) Exons   (0, 0)

(no "Exon" information available for 1ODH)

(-) 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    
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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:158
 aligned with GCM1_MOUSE | P70348 from UniProtKB/Swiss-Prot  Length:436

    Alignment length:158
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163        
          GCM1_MOUSE     14 LSWDINDVKLPQNVKTTDWFQEWPDSYVKHIYSSDDRNAQRHLSSWAMRNTNNHNSRILKKSCLGVVVCSRDCSTEEGRKIYLRPAICDKARQKQQRKSCPNCNGPLKLIPCRGHGGFPVTNFWRHDGRFIFFQSKGEHDHPRPETKLEAEARRAMKK  171
               SCOP domains d1odha_ A: Mgcm1                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------GCM-1odhA01 A:29-169                                                                                                                         -- Pfam domains
         Sec.struct. author ............................ee.....hhhhhh......eeee.......eeeee..eeee............ee....hhhhhhhhhhh........eeee..........eeeeee....eeeeee.........hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GCM  PDB: A:14-169 UniProt: 14-169                                                                                                                          -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1odh A   14 LSWDINDVKLPQNVKTTDWFQEWPDSYVKHIYSSDDRNAQRHLSSWAMRNTNNHNSRILKKSCLGVVVCSRDCSTEEGRKIYLRPAICDKARQKQQRKSCPNCNGPLKLIPCRGHGGFPVTNFWRHDGRFIFFQSKGEHDHPRPETKLEAEARRAMKK  171
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163        


Chain C from PDB  Type:DNA  Length:13
                                              
                1odh C 1001 CGATGCGGGTGCA 1013
                                  1010   


Chain D from PDB  Type:DNA  Length:13
                                              
                1odh D 1014 TGCACCCGCATCG 1026
                                  1023
   Legend:   → Mismatch (orange background)
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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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: WRKY-GCM1 (2)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GCM1_MOUSE | P70348)
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:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    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:0060018    astrocyte fate commitment    The commitment of a cells to a specific astrocyte fate and its restriction to develop only into an astrocyte.
    GO:0060670    branching involved in labyrinthine layer morphogenesis    The process in which the branches of the fetal placental villi are generated and organized. The villous part of the placenta is called the labyrinth layer.
    GO:0060706    cell differentiation involved in embryonic placenta development    The process in which a relatively unspecialized cell acquires specialized features of the embryonic placenta.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0060143    positive regulation of syncytium formation by plasma membrane fusion    Any process that increases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.
    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.
    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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