1ZRC | PD0670 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   4 CRYSTAL STRUCTURES OF CAP-DNA WITH ALL BASE-PAIR SUBSTITUTIONS AT POSITION 6, CAP-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 :   2.80

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)

*Molecule 1 - 5'- D(APTPTPTPCPGPAPAPAPAPAPTPGPTPGPAPT)-3'**
	Chains	:	W, Y
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'- D(CPTPAPGPAPTPCPAPCPAPTPTPTPTPTPCPGPAPAP APT)-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

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	W	X	Y	Z

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	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 , SER B:128	BINDING SITE FOR RESIDUE CMP A 210
2	AC2	SOFTWARE	SER A:128 , VAL B:49 , LEU B:61 , ILE B:70 , GLY B:71 , GLU B:72 , ARG B:82 , SER B:83 , ALA B:84 , ARG B:123 , THR B:127	BINDING SITE FOR RESIDUE CMP B 210

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

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

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

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:137-207
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 1ZRC)

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: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 d1zrca2 A:8-137 Catabolite gene activator protein, N-terminal domain                                                              d1zrca1 A:138-207                                                      SCOP domains
               CATH domains 1zrcA01 A:8-137 Jelly Rolls                                                                                                       1zrcA02 A: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...eeeeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....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
                 1zrc A   8 DPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYG 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: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 d1zrcb2 B:8-137 Catabolite gene activator protein, N-terminal domain                                                              d1zrcb1 B:138-207                                                      SCOP domains
               CATH domains 1zrcB01 B:8-137 Jelly Rolls                                                                                                       1zrcB02 B:138-207 'winged helix' repressor DNA binding domain          CATH domains
           Pfam domains (1) ------------cNMP_binding-1zrcB03 B:20-111                                                               -----------------------------------------------------Crp-1zrcB01 B:165-196           ----------- Pfam domains (1)
           Pfam domains (2) ------------cNMP_binding-1zrcB04 B:20-111                                                               -----------------------------------------------------Crp-1zrcB02 B:165-196           ----------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhh..........eee.........eeeee..eeeeee.....eeeeeee....ee..............eeee....eee..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........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
                 1zrc 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:17
                                                 
                 1zrc W  -8 ATTTCGAAAAATGTGAT   9
                                   ||2       
                                  -1|        
                                    1

Chain X from PDB  Type:DNA  Length:21
                                                     
                 1zrc X  13 CTAGATCACATTTTTCGAAAT  -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:17
                                                 
                 1zrc Y  -8 ATTTCGAAAAATGTGAT   9
                                   ||2       
                                  -1|        
                                    1

Chain Z from PDB  Type:DNA  Length:21
                                                     
                 1zrc Z  13 CTAGATCACATTTTTCGAAAT  -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 '\|'

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	1zrcA02	A:138-207
1b	1zrcB02	B:138-207

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Jelly Rolls (177)

[unclassified] (14)

2a	1zrcA01	A:8-137
2b	1zrcB01	B:8-137

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Crp (12)

Escherichia coli (strain K12) (10)

1a	Crp-1zrcB01	B:165-196
1b	Crp-1zrcB02	B:165-196

Clan: no clan defined [family: cNMP_binding] (41)

Family: cNMP_binding (41)

Escherichia coli (strain K12) (10)

2a	cNMP_binding-1zrcB03	B:20-111
2b	cNMP_binding-1zrcB04	B:20-111

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (5, 10)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (2, 4)

Gene Ontology (12, 12)

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