2WC2 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   NMR STRUCTURE OF CATABOLITE ACTIVATOR PROTEIN IN THE UNLIGANDED STATE

Authors :   N. Popovych, S. R. Tzeng, C. G. Kalodimos

Date :   06 Mar 09 (Deposition) - 21 Apr 09 (Release) - 21 Jul 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)

Keywords :   Transcription Regulator, Transctiption Factor, Transcription Regulation, Cyclic Nucleotide-Binding Protein, Camp-Binding, Transcription, Allosteric Protein, Catabolite Activator Protein, Nucleotide-Binding, Dna-Binding Protein, Camp, Activator, Acetylation, Dna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Popovych, S. R. Tzeng, M. Tonelli, R. H. Ebright, C. G. Kalodimos
Structural Basis For Camp-Mediated Allosteric Control Of The Catabolite Activator Protein.
Proc. Natl. Acad. Sci. Usa V. 106 6927 2009
PubMed-ID: 19359484 | Reference-DOI: 10.1073/PNAS.0900595106

Molecule 1 - CATABOLITE GENE ACTIVATOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	RESIDUES 2-210
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	469008
	Synonym	:	CATABOLITE ACTIVATOR PROTEIN, CAMP RECEPTOR PROTEIN, CAMP REGULATORY PROTEIN


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2WC2)

(no "Site" information available for 2WC2)

(no "SS Bond" information available for 2WC2)

(no "Cis Peptide Bond" information available for 2WC2)

(no "SAP(SNP)/Variant" information available for 2WC2)

NMR Structure (5, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	CRP_ECO57	24-124	2	A:23-123 B:23-123
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_ECO57	30-46	2	A:29-45 B:29-45
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_ECO57	71-89	2	A:70-88 B:70-88
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_ECO57	138-210	2	A:137-209 B:137-209
4	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	CRP_ECOLI	138-210	2	A:137-209 B:137-209
5	HTH_CRP_1	PS00042	Crp-type HTH domain signature.	CRP_ECO57	168-191	2	A:167-190 B:167-190
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 2WC2)

NMR Structure

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:209
 aligned with CRP_ECO57 | P0ACK0 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:209
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201         
            CRP_ECO57     2 VLGKPQTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 210
               SCOP domains d2wc2a1 A:1-137 automated matches                                                                                                        d2wc2a2 A:138-209 automated matches                                      SCOP domains
               CATH domains --------2wc2A01 A:9-137 Jelly Rolls                                                                                                      2wc2A02 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..hhhhhh......eeee...eeeeeeehhhhhhhh....hhhhhhhhhhhhhhh.................hhhhhhhhhhh...eee..eeeee.hhhhhhhhhh...hhhhhhhhhhhh.....ee..eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------CNMP_BINDING_3  PDB: A:23-123 UniProt: 24-124                                                        -------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------------------CNMP_BINDING_1   ------------------------CNMP_BINDING_2     ------------------------------------------------------------------------------HTH_CRP_1  PDB: A:167-19------------------- PROSITE (3)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_2  PDB: A:137-209 UniProt: 138-210                                PROSITE (1)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wc2 A   1 VLGKPQTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain A from PDB  Type:PROTEIN  Length:209
 aligned with CRP_ECOLI | P0ACJ8 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:209
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201         
            CRP_ECOLI     2 VLGKPQTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 210
               SCOP domains d2wc2a1 A:1-137 automated matches                                                                                                        d2wc2a2 A:138-209 automated matches                                      SCOP domains
               CATH domains --------2wc2A01 A:9-137 Jelly Rolls                                                                                                      2wc2A02 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..hhhhhh......eeee...eeeeeeehhhhhhhh....hhhhhhhhhhhhhhh.................hhhhhhhhhhh...eee..eeeee.hhhhhhhhhh...hhhhhhhhhhhh.....ee..eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------CNMP_BINDING_3  PDB: A:23-123 UniProt: 24-124                                                        -------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_2  PDB: A:137-209 UniProt: 138-210                                PROSITE (2)
                PROSITE (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ----------------------------CNMP_BINDING_1   ------------------------CNMP_BINDING_2     ------------------------------------------------------------------------------HTH_CRP_1  PDB: A:167-19------------------- PROSITE (4)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wc2 A   1 VLGKPQTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain B from PDB  Type:PROTEIN  Length:209
 aligned with CRP_ECO57 | P0ACK0 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:209
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201         
            CRP_ECO57     2 VLGKPQTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 210
               SCOP domains d2wc2b1 B:1-137 automated matches                                                                                                        d2wc2b2 B:138-209 automated matches                                      SCOP domains
               CATH domains --------2wc2B01 B:9-137 Jelly Rolls                                                                                                      2wc2B02 B:138-209 'winged helix' repressor DNA binding domain            CATH domains
           Pfam domains (1) -------------------cNMP_binding-2wc2B03 B:20-111                                                               -----------------------------------------------------Crp-2wc2B01 B:165-196           ------------- Pfam domains (1)
           Pfam domains (2) -------------------cNMP_binding-2wc2B04 B:20-111                                                               -----------------------------------------------------Crp-2wc2B02 B:165-196           ------------- Pfam domains (2)
         Sec.struct. author .......hhhhhhhhh..eeeee....eee.......eeeeeee.eeeeeee.....eeeeeeee...ee..hhhhhh......eeee...eeeeeeehhhhhhhh....hhhhhhhhhhhhhhh.................hhhhhhhhhhh...eee..eeeee.hhhhhhhhhh...hhhhhhhhhhhh.....ee..eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------CNMP_BINDING_3  PDB: B:23-123 UniProt: 24-124                                                        -------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------------------------CNMP_BINDING_1   ------------------------CNMP_BINDING_2     ------------------------------------------------------------------------------HTH_CRP_1  PDB: B:167-19------------------- PROSITE (3)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_2  PDB: B:137-209 UniProt: 138-210                                PROSITE (1)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wc2 B   1 VLGKPQTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain B from PDB  Type:PROTEIN  Length:209
 aligned with CRP_ECOLI | P0ACJ8 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:209
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201         
            CRP_ECOLI     2 VLGKPQTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 210
               SCOP domains d2wc2b1 B:1-137 automated matches                                                                                                        d2wc2b2 B:138-209 automated matches                                      SCOP domains
               CATH domains --------2wc2B01 B:9-137 Jelly Rolls                                                                                                      2wc2B02 B:138-209 'winged helix' repressor DNA binding domain            CATH domains
           Pfam domains (1) -------------------cNMP_binding-2wc2B03 B:20-111                                                               -----------------------------------------------------Crp-2wc2B01 B:165-196           ------------- Pfam domains (1)
           Pfam domains (2) -------------------cNMP_binding-2wc2B04 B:20-111                                                               -----------------------------------------------------Crp-2wc2B02 B:165-196           ------------- Pfam domains (2)
         Sec.struct. author .......hhhhhhhhh..eeeee....eee.......eeeeeee.eeeeeee.....eeeeeeee...ee..hhhhhh......eeee...eeeeeeehhhhhhhh....hhhhhhhhhhhhhhh.................hhhhhhhhhhh...eee..eeeee.hhhhhhhhhh...hhhhhhhhhhhh.....ee..eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------CNMP_BINDING_3  PDB: B:23-123 UniProt: 24-124                                                        -------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_2  PDB: B:137-209 UniProt: 138-210                                PROSITE (2)
                PROSITE (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ----------------------------CNMP_BINDING_1   ------------------------CNMP_BINDING_2     ------------------------------------------------------------------------------HTH_CRP_1  PDB: B:167-19------------------- PROSITE (4)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wc2 B   1 VLGKPQTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Winged helix DNA-binding domain (576)

Family: automated matches (118)

Protein domain: automated matches (118)

Escherichia coli [TaxId: 469008] (1)

1a	d2wc2a2	A:138-209
1b	d2wc2b2	B:138-209

Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: cAMP-binding domain-like (99)

Family: cAMP-binding domain (78)

Protein domain: automated matches (22)

Escherichia coli [TaxId: 469008] (1)

2a	d2wc2a1	A:1-137
2b	d2wc2b1	B:1-137

NMR Structure

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)

Escherichia coli. Organism_taxid: 469008. (1)

1a	2wc2A02	A:138-209
1b	2wc2B02	B:138-209

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Jelly Rolls (177)

Escherichia coli. Organism_taxid: 469008. (1)

2a	2wc2A01	A:9-137
2b	2wc2B01	B:9-137

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Crp (12)

Escherichia coli O157:H7 (1)

1a	Crp-2wc2B01	B:165-196
1b	Crp-2wc2B02	B:165-196

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

Family: cNMP_binding (41)

Escherichia coli O157:H7 (1)

2a	cNMP_binding-2wc2B03	B:20-111
2b	cNMP_binding-2wc2B04	B:20-111

NMR Structure(hide GO term definitions)

Chain A,B (CRP_ECO57 | P0ACK0)

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: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: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: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.

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.

NMR Structure
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	Cis Peptide Bonds
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	2wc2
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(no "Related Entries Specified in the PDB File" available for 2WC2)

Description

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Ligands, Modified Residues, Ions (0, 0)

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SCOP Domains (2, 4)

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