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(-) Description

Title :  PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES
 
Authors :  S. Chen, R. H. Ebright, H. M. Berman
Date :  18 Mar 03  (Deposition) - 08 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Protein-Dna Complex, Cap, Cap-Dna, Catabolite Gene Activator Protein, Camp Receptor Protein, Crp, Gene Regulation/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chen, A. Gunasekera, X. Zhang, T. A. Kunkel, R. H. Ebright, H. M. Berman
Indirect Readout Of Dna Sequence At The Primary-Kink Site In The Cap-Dna Complex: Alteration Of Dna Binding Specificity Through Alteration Of Dna Kinking
J. Mol. Biol. V. 314 75 2001
PubMed-ID: 11724533  |  Reference-DOI: 10.1006/JMBI.2001.5090
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'- D(*CP*TP*AP*GP*AP*TP*CP*GP*CP*AP*TP*TP*TP*TP*T)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - CATABOLITE GENE ACTIVATOR PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CAP, CAMP RECEPTOR PROTEIN, CAMP-REGULATORY PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CMP2Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CMP4Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:49 , LEU A:61 , ILE A:70 , GLY A:71 , GLU A:72 , LEU A:73 , ARG A:82 , SER A:83 , ARG A:123 , THR A:127 , SER A:128BINDING SITE FOR RESIDUE CMP A 1
2AC2SOFTWARELYS A:57 , GLU A:58 , ALA A:135 , PHE A:136 , GLN A:170 , GLY A:173 , GLN A:174 , CYS A:178 , SER A:179 , ARG A:180 , HOH A:230 , DA C:9BINDING SITE FOR RESIDUE CMP A 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O3S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1O3S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O3S)

(-) PROSITE Motifs  (5, 5)

Asymmetric Unit (5, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.CRP_ECOLI24-124  1A:23-123
2CNMP_BINDING_1PS00888 Cyclic nucleotide-binding domain signature 1.CRP_ECOLI30-46  1A:29-45
3CNMP_BINDING_2PS00889 Cyclic nucleotide-binding domain signature 2.CRP_ECOLI71-89  1A:70-88
4HTH_CRP_2PS51063 Crp-type HTH domain profile.CRP_ECOLI138-210  1A:137-207
5HTH_CRP_1PS00042 Crp-type HTH domain signature.CRP_ECOLI168-191  1A:167-190
Biological Unit 1 (5, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.CRP_ECOLI24-124  2A:23-123
2CNMP_BINDING_1PS00888 Cyclic nucleotide-binding domain signature 1.CRP_ECOLI30-46  2A:29-45
3CNMP_BINDING_2PS00889 Cyclic nucleotide-binding domain signature 2.CRP_ECOLI71-89  2A:70-88
4HTH_CRP_2PS51063 Crp-type HTH domain profile.CRP_ECOLI138-210  2A:137-207
5HTH_CRP_1PS00042 Crp-type HTH domain signature.CRP_ECOLI168-191  2A:167-190

(-) Exons   (0, 0)

(no "Exon" information available for 1O3S)

(-) 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:200
 aligned with CRP_ECOLI | P0ACJ8 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:200
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208
            CRP_ECOLI     9 DPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYG 208
               SCOP domains d1o3sa2 A:8-137 Catabolite gene activator protein, N-terminal domain                                                              d1o3sa1 A:138-207                                                      SCOP domains
               CATH domains -1o3sA01 A:9-137 Jelly Rolls                                                                                                      1o3sA02 A:138-206 'winged helix' repressor DNA binding domain        - CATH domains
               Pfam domains ------------cNMP_binding-1o3sA02 A:20-111                                                               -----------------------------------------------------Crp-1o3sA01 A:165-196           ----------- Pfam domains
         Sec.struct. author .hhhhhhhh..eeeee....eee.......eeeeeee..eeeeee.....eeeeeee...eee..............eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....eee..eeeee.hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------CNMP_BINDING_3  PDB: A:23-123 UniProt: 24-124                                                        -------------HTH_CRP_2  PDB: A:137-207 UniProt: 138-210                              PROSITE (1)
                PROSITE (2) ---------------------CNMP_BINDING_1   ------------------------CNMP_BINDING_2     ------------------------------------------------------------------------------HTH_CRP_1  PDB: A:167-19----------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o3s A   8 DPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRDTVGRILKMLEDQNLISAHGKTIVVYG 207
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207


Chain B from PDB  Type:DNA  Length:11
                                           
                 1o3s B  -2 AAAAATGCGAT   9
                             ||      8 
                            -1|        
                              1        


Chain C from PDB  Type:DNA  Length:15
                                               
                 1o3s C  13 CTAGATCGCATTTTT  -2
                            |||||||||4|||||
                           13||||||||4|||||
                            12||||||| 3||||
                             11||||||  2|||
                              10|||||   1||
                                9||||   -1|
                                 8|||    -2
                                  7||      
                                   6|      
                                    5
   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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Clan: no clan defined [family: cNMP_binding] (41)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (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:0003700    DNA-binding transcription factor activity    A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
    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).
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 | P0ACJ8: 1cgp 1g6n 1hw5 1i5z 1i6x 1j59 1lb2 1o3q 1o3r 1o3t 1run 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

1o3q 1o3r 1o3t