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Title :   CRYSTAL STRUCTURE OF THE APO D138L CAP MUTANT

Authors :   H. Sharma, J. Wang, J. Kong, S. Yu, T. Steitz

Date :   17 Jan 09 (Deposition) - 08 Sep 09 (Release) - 20 Oct 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B

Keywords :   Helix-Turn-Helix, Transcription, Camp, Allostery, Acetylation, Activator, Camp-Binding, Dna-Binding, Nucleotide-Binding, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Sharma, S. Yu, J. Kong, J. Wang, T. A. Steitz
Structure Of Apo-Cap Reveals That Large Conformational Changes Are Necessary For Dna Binding
Proc. Natl. Acad. Sci. Usa V. 106 16604 2009
PubMed-ID: 19805344 | Reference-DOI: 10.1073/PNAS.0908380106
(for further references see the PDB file header)

Molecule 1 - CATABOLITE GENE ACTIVATOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	DH5A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	B3357, CAP, CRP, CSM, JW5702
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI K-12
	Organism Taxid	:	83333
	Strain	:	DH5A
	Synonym	:	CAMP RECEPTOR PROTEIN, CAMP REGULATORY PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	PRO	2	Mod. Amino Acid	PROLINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:28 , GLN A:32 , LYS A:52	BINDING SITE FOR RESIDUE PRO A 210
2	AC2	SOFTWARE	VAL A:108 , ASN A:109 , HOH A:245	BINDING SITE FOR RESIDUE PRO A 211

(no "SS Bond" information available for 3FWE)

Asymmetric/Biological Unit

No.	Residues
1	Val A:131	-	Gly A:132
2	Gly B:79	-	Gln B:80

(no "SAP(SNP)/Variant" information available for 3FWE)

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:137-208
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 3FWE)

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:204
 aligned with CRP_ECOLI | P0ACJ8 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:204
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206    
            CRP_ECOLI     7 QTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGTR 210
               SCOP domains d3fwea1 A:6-137 Catabolite gene activator protein, N-terminal domain                                                                d3fwea2 A:138-207 automated matches                                   -- SCOP domains
               CATH domains 3fweA01 A:6-131 Jelly Rolls                                                                                                   3fweA02 A:132-207 'winged helix' repressor DNA binding domain               -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhh.eeeee....eee.......eeeeeee.eeeeeee.....eeeeeeee...ee..hhhhh.......eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...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
                 3fwe A   6 QTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLLVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGPP 211
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205 || 
                                                                                                                                                                                                                                   207| 
                                                                                                                                                                                                                                    210

Chain B from PDB  Type:PROTEIN  Length:203
 aligned with CRP_ECOLI | P0ACJ8 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:203
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   
            CRP_ECOLI     7 QTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGT 209
               SCOP domains d3fweb1 B:6-137 Catabolite gene activator protein, N-terminal domain                                                                d3fweb2 B:138-208 automated matches                                     SCOP domains
               CATH domains 3fweB01 B:6-131 Jelly Rolls                                                                                                   3fweB02 B:132-208 'winged helix' repressor DNA binding domain                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.eeeee....eee.......eeeeeee..eeeeee.....eeeeeee....eehhhhhhh.......eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...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:137-208 UniProt: 138-210                               PROSITE (1)
                PROSITE (2) -----------------------CNMP_BINDING_1   ------------------------CNMP_BINDING_2     ------------------------------------------------------------------------------HTH_CRP_1  PDB: B:167-19------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fwe B   6 QTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLLVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGT 208
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205

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(

)

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 K-12 [TaxId: 83333] (13)

1a	d3fwea2	A:138-207
1b	d3fweb2	B:138-208

Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: cAMP-binding domain-like (99)

Family: cAMP-binding domain (78)

Protein domain: Catabolite gene activator protein, N-terminal domain (28)

Escherichia coli [TaxId: 562] (28)

2a	d3fwea1	A:6-137
2b	d3fweb1	B:6-137

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)

Escherichia coli k-12. Organism_taxid: 83333. Strain: dh5a. (1)

1a	3fweB02	B:132-208
1b	3fweA02	A:132-207

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Jelly Rolls (177)

Escherichia coli k-12. Organism_taxid: 83333. Strain: dh5a. (1)

2a	3fweA01	A:6-131
2b	3fweB01	B:6-131

(no "Pfam Domain" information available for 3FWE)

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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	Cis Peptide Bonds
		Gly B:79 - Gln B:80	[ RasMol ]
		Val A:131 - Gly A:132	[ RasMol ]

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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (5, 10)

Exons (0, 0)

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