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(-) Description

Title :  4 CRYSTAL STRUCTURES OF CAP-DNA WITH ALL BASE-PAIR SUBSTITUTIONS AT POSITION 6, CAP-[6C;17G]ICAP38 DNA
 
Authors :  H. M. Berman, A. A. Napoli
Date :  19 May 05  (Deposition) - 21 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,W,X,Y,Z
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 :  A. A. Napoli, C. L. Lawson, R. H. Ebright, H. M. Berman
Indirect Readout Of Dna Sequence At The Primary-Kink Site In The Cap-Dna Complex: Recognition Of Pyrimidine-Purine And Purine-Purine Steps.
J. Mol. Biol. V. 357 173 2006
PubMed-ID: 16427082  |  Reference-DOI: 10.1016/J.JMB.2005.12.051
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3'
    Chains: W, Y
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'- D(*CP*TP*AP*GP*AP*TP*CP*GP*CP*AP*TP*TP*TP*TP*TP*CP*GP*AP*AP *AP*T)-3'
    Chains: X, Z
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - CATABOLITE GENE ACTIVATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PAKCRP1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CRP, CAP, CSM
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CAMP RECEPTOR PROTEIN, CAMP-REGULATORY PROTEIN

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABWXYZ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1CMP4Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
2DIO5Ligand/Ion1,4-DIETHYLENE DIOXIDE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:49 , GLY A:71 , GLU A:72 , LEU A:73 , ARG A:82 , SER A:83 , ALA A:84 , THR A:127 , HOH A:2625 , HOH A:2626 , HOH A:2656 , LEU B:124 , SER B:128BINDING SITE FOR RESIDUE CMP A 622
2AC2SOFTWARESER A:128 , VAL B:49 , ILE B:70 , GLY B:71 , GLU B:72 , LEU B:73 , ARG B:82 , SER B:83 , ALA B:84 , THR B:127 , HOH B:3628 , HOH B:3639BINDING SITE FOR RESIDUE CMP B 1622
3AC3SOFTWARELYS A:57 , GLU A:58 , GLN A:170 , GLY A:173 , GLN A:174 , GLY A:177 , CYS A:178 , ARG A:180 , HOH A:2639 , ALA B:135BINDING SITE FOR RESIDUE CMP A 2622
4AC4SOFTWAREALA A:135 , LYS B:57 , GLU B:58 , GLN B:170 , GLY B:173 , GLN B:174 , GLY B:177 , CYS B:178 , SER B:179 , ARG B:180 , HOH B:3690 , DA Z:9BINDING SITE FOR RESIDUE CMP B 3622
5AC5SOFTWAREALA B:144BINDING SITE FOR RESIDUE DIO B 301
6AC6SOFTWARELYS B:130 , ARG B:142 , THR B:146 , ILE B:175 , VAL B:176BINDING SITE FOR RESIDUE DIO B 302
7AC7SOFTWARELEU A:148 , LEU A:195 , VAL A:205BINDING SITE FOR RESIDUE DIO A 303
8AC8SOFTWARELEU A:11 , PHE A:14 , TYR A:41 , PHE A:69 , ILE A:112 , ARG A:115 , ARG A:209BINDING SITE FOR RESIDUE DIO A 304
9AC9SOFTWARELYS A:130 , ARG A:142 , THR A:146 , ILE A:175 , VAL A:176 , HOH A:2661BINDING SITE FOR RESIDUE DIO A 305

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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:137-207
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 1ZRF)

(-) 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:203
 aligned with CRP_ECOLI | P0ACJ8 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:203
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207   
            CRP_ECOLI     8 TDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 210
               SCOP domains d1zrfa2 A:7-137 Catabolite gene activator protein, N-terminal domain                                                               d1zrfa1 A:138-209                                                        SCOP domains
               CATH domains 1zrfA01 A:7-137 Jelly Rolls                                                                                                        1zrfA02 A:138-209 'winged helix' repressor DNA binding domain            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..eeeee....eee.......eeeeeee.eeeeeee.....eeeeeeee...ee..............eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....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:137-209 UniProt: 138-210                                PROSITE (1)
                PROSITE (2) ----------------------CNMP_BINDING_1   ------------------------CNMP_BINDING_2     ------------------------------------------------------------------------------HTH_CRP_1  PDB: A:167-19------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zrf A   7 TDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 209
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   


Chain B 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 d1zrfb2 B:8-137 Catabolite gene activator protein, N-terminal domain                                                              d1zrfb1 B:138-207                                                      SCOP domains
               CATH domains 1zrfB01 B:8-137 Jelly Rolls                                                                                                       1zrfB02 B:138-207 'winged helix' repressor DNA binding domain          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..eeeee....eee.......eeeeeee.eeeeeee.....eeeeeeee...ee..............eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee..eeeee.hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------CNMP_BINDING_3  PDB: B:23-123 UniProt: 24-124                                                        -------------HTH_CRP_2  PDB: B:137-207 UniProt: 138-210                              PROSITE (1)
                PROSITE (2) ---------------------CNMP_BINDING_1   ------------------------CNMP_BINDING_2     ------------------------------------------------------------------------------HTH_CRP_1  PDB: B:167-19----------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zrf B   8 DPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYG 207
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207


Chain W from PDB  Type:DNA  Length:15
                                               
                 1zrf W  -6 TTCGAAAAATGCGAT   9
                                 ||  4     
                                -1|        
                                  1        


Chain X from PDB  Type:DNA  Length:21
                                                     
                 1zrf X  13 CTAGATCGCATTTTTCGAAAT  -8
                            |||||||||4||||||||-7|
                           13||||||||4|||||||-6||
                            12||||||| 3|||||||-7|
                             11||||||  2|||||| -8
                              10|||||   1|||||   
                                9||||   -1||||   
                                 8|||    -2|||   
                                  7||     -3||   
                                   6|      -4|   
                                    5       -5   


Chain Y from PDB  Type:DNA  Length:16
                                                
                 1zrf Y  -7 TTTCGAAAAATGCGAT   9
                                  || 3      
                                 -1|        
                                   1        


Chain Z from PDB  Type:DNA  Length:21
                                                     
                 1zrf Z  13 CTAGATCGCATTTTTCGAAAT  -8
                            |||||||||4||||||||-7|
                           13||||||||4|||||||-6||
                            12||||||| 3|||||||-7|
                             11||||||  2|||||| -8
                              10|||||   1|||||   
                                9||||   -1||||   
                                 8|||    -2|||   
                                  7||     -3||   
                                   6|      -4|   
                                    5       -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, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ZRF)

(-) 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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  1zrf
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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 1o3s 1o3t 1run 1ruo 1zrc 1zrd 1zre 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

1zrc 4 CRYSTAL STRUCTURES OF CAP-DNA WITH ALL BASE-PAIR SUBSTITUTIONS AT POSITION 6, CAP-ICAP38 DNA
1zrd 4 CRYSTAL STRUCTURES OF CAP-DNA WITH ALL BASE-PAIR SUBSTITUTIONS AT POSITION 6, CAP-[6A;17T]ICAP38 DNA
1zre 4 CRYSTAL STRUCTURES OF CAP-DNA WITH ALL BASE-PAIR SUBSTITUTIONS AT POSITION 6, CAP-[6G;17C]ICAP38 DNA