1O3T | PD0401 - JenaLib

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Title :   PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES

Authors :   S. Chen, J. Vojtechovsky, G. N. Parkinson, R. H. Ebright, H. M. Berman

Date :   18 Mar 03 (Deposition) - 08 Apr 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

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, J. Vojtechovsky, G. N. Parkinson, R. H. Ebright, H. M. Berman
Indirect Readout Of Dna Sequence At The Primary-Kink Site In The Cap-Dna Complex: Dna Binding Specificity Based On Energetics Of Dna Kinking
J. Mol. Biol. V. 314 63 2001
PubMed-ID: 11724532 | Reference-DOI: 10.1006/JMBI.2001.5089
(for further references see the PDB file header)

*Molecule 1 - 5'-D(GPCPGPAPAPAPAPAPTPGPCPGPAPT)- 3'*
	Chains	:	C, F
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'- D(CPTPAPGPAPTPCPGPCPAPTPTPTPTPTPCPG)-3'**
	Chains	:	D, E
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - CATABOLITE GENE ACTIVATOR PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	CAP, CAMP RECEPTOR PROTEIN, CAMP-REGULATORY PROTEIN

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CMP	2	Ligand/Ion	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:124 , SER A:128 , ILE B:30 , VAL B:49 , SER B:62 , GLY B:71 , GLU B:72 , LEU B:73 , ARG B:82 , SER B:83 , ALA B:84 , ARG B:123 , THR B:127	BINDING SITE FOR RESIDUE CMP B 761
2	AC2	SOFTWARE	VAL A:49 , LEU A:61 , ILE A:70 , GLY A:71 , GLU A:72 , LEU A:73 , ARG A:82 , SER A:83 , ALA A:84 , THR A:127 , LEU B:124 , SER B:128	BINDING SITE FOR RESIDUE CMP A 762

(no "SS Bond" information available for 1O3T)

(no "Cis Peptide Bond" information available for 1O3T)

(no "SAP(SNP)/Variant" information available for 1O3T)

Asymmetric/Biological Unit (5, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	CRP_ECOLI	24-124	2	A:23-123 B:23-123
2	CNMP_BINDING_1	PS00888	Cyclic nucleotide-binding domain signature 1.	CRP_ECOLI	30-46	2	A:29-45 B:29-45
3	CNMP_BINDING_2	PS00889	Cyclic nucleotide-binding domain signature 2.	CRP_ECOLI	71-89	2	A:70-88 B:70-88
4	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	CRP_ECOLI	138-210	2	A:137-207 B:137-205
5	HTH_CRP_1	PS00042	Crp-type HTH domain signature.	CRP_ECOLI	168-191	2	A:167-190 B:167-190

(no "Exon" information available for 1O3T)

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:199
 aligned with CRP_ECOLI | P0ACJ8 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:199
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199         
            CRP_ECOLI    10 PTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYG 208
               SCOP domains d1o3ta2 A:9-137 Catabolite gene activator protein, N-terminal domain                                                             d1o3ta1 A:138-207                                                      SCOP domains
               CATH domains 1o3tA01 A:9-137 Jelly Rolls                                                                                                      1o3tA02 A:138-205 'winged helix' repressor DNA binding domain       -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..eeee....eee.........eeeee..eeeeee.....eeeeeee....ee..............eee....eeeee.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....ee....eee..hhhhhhhhhh.hhhhhhhhhhhhhhh........eee... 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
                 1o3t A   9 PTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYG 207
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198

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 d1o3tb2 B:9-137 Catabolite gene activator protein, N-terminal domain                                                             d1o3tb1 B:138-205                                                    SCOP domains
               CATH domains 1o3tB01 B:9-137 Jelly Rolls                                                                                                      1o3tB02 B:138-205 'winged helix' repressor DNA binding domain        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.......................eeeee..eeeeee.....eeeeee.....ee..............eeee....ee...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....ee..ee....hhhhhhhhhh.hhhhhhhhhhhhhhhh........... 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
                 1o3t 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
                                              
                 1o3t C  -5 GCGAAAAATGCGAT   9
                                ||   5    
                               -1|        
                                 1

Chain D from PDB  Type:DNA  Length:17
                                                 
                 1o3t D  13 CTAGATCGCATTTTTCG  -4
                            |||||||||4|||||||
                           13||||||||4|||||||
                            12||||||| 3||||||
                             11||||||  2|||||
                              10|||||   1||||
                                9||||   -1|||
                                 8|||    -2||
                                  7||     -3|
                                   6|      -4
                                    5

Chain E from PDB  Type:DNA  Length:17
                                                 
                 1o3t E  10 CTAGATCGCATTTTTCG  26
                                    19

Chain F from PDB  Type:DNA  Length:14
                                              
                 1o3t F  27 GCGAAAAATGCGAT  14
                            ||||||||18||||
                           27|||||||18||||
                            26|||||||17|||
                             25|||||| 16||
                              24|||||  15|
                               23||||   14
                                22|||     
                                 21||     
                                  20|     
                                   19

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

[unclassified] (77)

1a	1o3tA02	A:138-205
1b	1o3tB02	B:138-205

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Jelly Rolls (177)

[unclassified] (14)

2a	1o3tA01	A:9-137
2b	1o3tB01	B:9-137

(no "Pfam Domain" information available for 1O3T)

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.

Asymmetric/Biological Unit
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	1o3t
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Description

Compounds

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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PROSITE Motifs (5, 10)

Exons (0, 0)

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Gene Ontology (12, 12)

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