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(-) Description

Title :  CATABOLITE GENE ACTIVATOR PROTEIN (CAP)/DNA COMPLEX + ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
 
Authors :  G. N. Parkinson, A. Gunasekera, J. Vojtechovsky, X. Zhang, T. A. Kunkel, H. M. Berman, R. H. Ebright
Date :  26 May 96  (Deposition) - 10 Jan 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Transcription Regulation; 3D-Structure; Dna-Binding; Camp- Binding; Activator, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Parkinson, A. Gunasekera, J. Vojtechovsky, X. Zhang, T. A. Kunkel, H. Berman, R. H. Ebright
Aromatic Hydrogen Bond In Sequence-Specific Protein Dna Recognition.
Nat. Struct. Biol. V. 3 837 1996
PubMed-ID: 8836098  |  Reference-DOI: 10.1038/NSB1096-837
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*GP*CP*GP*AP*AP*AP*AP*AP*TP*GP*TP*GP*AP*T)-3')
    ChainsC, E
    EngineeredYES
    SyntheticYES
 
Molecule 2 - DNA (5'- D(*CP*TP*AP*GP*AP*TP*CP*AP*CP*AP*TP*TP*TP*TP*TP*CP*G )-3')
    ChainsD, F
    EngineeredYES
    SyntheticYES
 
Molecule 3 - PROTEIN (CATABOLITE GENE ACTIVATOR PROTEIN (CAP) )
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CMP2Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:124 , SER A:128 , VAL B:49 , SER B:62 , GLY B:71 , GLU B:72 , LEU B:73 , ARG B:82 , SER B:83 , ALA B:84 , THR B:127BINDING SITE FOR RESIDUE CMP B 678
2AC2SOFTWARESER A:62 , ILE A:70 , GLY A:71 , GLU A:72 , LEU A:73 , ARG A:82 , SER A:83 , ALA A:84 , THR A:127 , HOH A:483 , HOH A:655 , LEU B:124 , SER B:128BINDING SITE FOR RESIDUE CMP A 679

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (5, 10)

Asymmetric/Biological Unit (5, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.CRP_ECOLI24-124
 
  2A:23-123
B:23-123
2CNMP_BINDING_1PS00888 Cyclic nucleotide-binding domain signature 1.CRP_ECOLI30-46
 
  2A:29-45
B:29-45
3CNMP_BINDING_2PS00889 Cyclic nucleotide-binding domain signature 2.CRP_ECOLI71-89
 
  2A:70-88
B:70-88
4HTH_CRP_2PS51063 Crp-type HTH domain profile.CRP_ECOLI138-210
 
  2A:137-209
B:137-205
5HTH_CRP_1PS00042 Crp-type HTH domain signature.CRP_ECOLI168-191
 
  2A:167-190
B:167-190

(-) Exons   (0, 0)

(no "Exon" information available for 1RUN)

(-) 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:201
 aligned with CRP_ECOLI | P0ACJ8 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:201
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209 
            CRP_ECOLI    10 PTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 210
               SCOP domains d1runa2 A:9-137 Catabolite gene activator protein, N-terminal domain                                                             d1runa1 A:138-209                                                        SCOP domains
               CATH domains 1runA01 A:9-137 Jelly Rolls                                                                                                      1runA02 A:138-205 'winged helix' repressor DNA binding domain       ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh......ee..............eeeee...eeeeeee.....eeeeeeee...ee..............eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eeee.hhhhhhhhhh.hhhhhhhhhhhh.....eee..eeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------CNMP_BINDING_3  PDB: A:23-123 UniProt: 24-124                                                        -------------HTH_CRP_2  PDB: A:137-209 UniProt: 138-210                                PROSITE (1)
                PROSITE (2) --------------------CNMP_BINDING_1   ------------------------CNMP_BINDING_2     ------------------------------------------------------------------------------HTH_CRP_1  PDB: A:167-19------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1run A   9 PTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 209
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208 

Chain B from PDB  Type:PROTEIN  Length:197
 aligned with CRP_ECOLI | P0ACJ8 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:197
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       
            CRP_ECOLI    10 PTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVV 206
               SCOP domains d1runb2 B:9-137 Catabolite gene activator protein, N-terminal domain                                                             d1runb1 B:138-205                                                    SCOP domains
               CATH domains 1runB01 B:9-137 Jelly Rolls                                                                                                      1runB02 B:138-205 'winged helix' repressor DNA binding domain        CATH domains
           Pfam domains (1) -----------cNMP_binding-1runB03 B:20-111                                                               -----------------------------------------------------Crp-1runB01 B:165-196           --------- Pfam domains (1)
           Pfam domains (2) -----------cNMP_binding-1runB04 B:20-111                                                               -----------------------------------------------------Crp-1runB02 B:165-196           --------- Pfam domains (2)
         Sec.struct. author hhhhhhhhh..........eee.......eeeeeee.eeeeeee.....eeeeeeee...ee..hhhhh.......eeee....eeeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee....eeee.hhhhhhhhhh.hhhhhhhhhhhhhhh.......ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------CNMP_BINDING_3  PDB: B:23-123 UniProt: 24-124                                                        -------------HTH_CRP_2  PDB: B:137-205 UniProt: 138-210                            PROSITE (1)
                PROSITE (2) --------------------CNMP_BINDING_1   ------------------------CNMP_BINDING_2     ------------------------------------------------------------------------------HTH_CRP_1  PDB: B:167-19--------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1run B   9 PTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVV 205
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       

Chain C from PDB  Type:DNA  Length:14
                                              
                 1run C  -5 GCGAAAAATGTGAT   9
                                ||   5    
                               -1|        
                                 1        

Chain D from PDB  Type:DNA  Length:17
                                                 
                 1run D  10 CTAGATCACATTTTTCG  26
                                    19       

Chain E from PDB  Type:DNA  Length:14
                                              
                 1run E  27 GCGAAAAATGTGAT  14
                            ||||||||18||||
                           27|||||||18||||
                            26|||||||17|||
                             25|||||| 16||
                              24|||||  15|
                               23||||   14
                                22|||     
                                 21||     
                                  20|     
                                   19     

Chain F from PDB  Type:DNA  Length:17
                                                 
                 1run F  13 CTAGATCACATTTTTCG  -4
                            |||||||||4|||||||
                            ||||||||5||||||||
                           13||||||| 4|||||||
                            12||||||  3||||||
                             11|||||   2|||||
                              10||||    1||||
                                9|||    -1|||
                                 8||     -2||
                                  7|      -3|
                                   6       -4

   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

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CRP_ECOLI | P0ACJ8)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0030552    cAMP binding    Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.
biological process
    GO:0045013    carbon catabolite repression of transcription    A transcription regulation process in which the presence of one carbon source leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other carbon sources. Carbon catabolite repression is a mechanism of genetic regulation which the accumulation of catabolites of one substance in the cell represses the formation of enzymes that contribute to the catabolism of other substances.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CRP_ECOLI | P0ACJ81cgp 1g6n 1hw5 1i5z 1i6x 1j59 1lb2 1o3q 1o3r 1o3s 1o3t 1ruo 1zrc 1zrd 1zre 1zrf 2cgp 2gap 2gzw 2wc2 3fwe 3hif 3iyd 3kcc 3n4m 3qop 3rdi 3rou 3rpq 3ryp 3ryr 4bh9 4bhp 4ft8 4hzf 4i01 4i02 4i09 4i0a 4i0b 4r8h 5ciz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RUN)