1HW5 - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

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Title :   THE CAP/CRP VARIANT T127L/S128A

Authors :   S. Y. Chu, M. Tordova, G. L. Gilliland, I. Gorshkova, Y. Shi

Date :   09 Jan 01 (Deposition) - 17 Jan 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.82

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

Keywords :   Camp Receptor Protein, Catabolite Activator Protein (Cap) Transcription, Allostery, Camp, Cyclic Amp Mutant, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Y. Chu, M. Tordova, G. L. Gilliland, I. Gorshkova, Y. Shi, S. Wang, F. P. Schwarz
The Structure Of The T127L/S128A Mutant Of Camp Receptor Protein Facilitates Promoter Site Binding
J. Biol. Chem. V. 276 11230 2001
PubMed-ID: 11124966 | Reference-DOI: 10.1074/JBC.M010428200
(for further references see the PDB file header)

Molecule 1 - CATABOLITE GENE ACTIVATOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI K12
	Expression System Strain	:	K12
	Expression System Taxid	:	83333
	Expression System Vector Type	:	PLASMID
	Gene	:	CRP/CAP
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	CAMP RECEPTOR PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL B:49 , LEU B:61 , SER B:62 , ILE B:70 , GLY B:71 , GLU B:72 , LEU B:73 , ARG B:82 , SER B:83 , ALA B:84 , VAL B:86 , ARG B:123 , LEU B:127 , HOH B:1003 , HOH B:1008 , HOH B:1060	BINDING SITE FOR RESIDUE CMP B 210
2	AC2	SOFTWARE	SER A:62 , ILE A:70 , GLY A:71 , GLU A:72 , LEU A:73 , ARG A:82 , SER A:83 , ALA A:84 , VAL A:86 , LEU A:127 , HOH A:1001 , HOH A:1014 , HOH A:1066	BINDING SITE FOR RESIDUE CMP A 210
3	AC3	SOFTWARE	LYS A:57 , GLU A:58 , GLN A:170 , GLY A:173 , GLN A:174 , GLY A:177 , CYS A:178 , SER A:179 , ARG A:180 , HOH A:1102 , HOH A:1207 , ALA B:135 , PHE B:136 , HOH B:1089	BINDING SITE FOR RESIDUE CMP A 211

(no "SS Bond" information available for 1HW5)

Asymmetric/Biological Unit

No.	Residues
1	Lys B:4	-	Pro B:5

(no "SAP(SNP)/Variant" information available for 1HW5)

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:137-208 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 1HW5)

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:208
 aligned with CRP_ECOLI | P0ACJ8 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:208
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201        
            CRP_ECOLI     2 VLGKPQTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGT 209
               SCOP domains d1hw5a2 A:1-137 Catabolite gene activator protein, N-terminal domain                                                                     d1hw5a1 A:138-208                                                       SCOP domains
               CATH domains --------1hw5A01 A:9-137 Jelly Rolls                                                                                                      1hw5A02 A:138-205 'winged helix' repressor DNA binding domain       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh..eeeee....eee.......eeeeeee.eeeeeee.....eeeeeeee...ee.hhhhh........eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeee.hhhhhhhhhh.hhhhhhhhhhhhhhh..ee...eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------CNMP_BINDING_3  PDB: A:23-123 UniProt: 24-124                                                        -------------HTH_CRP_2  PDB: A:137-208 UniProt: 138-210                               PROSITE (1)
                PROSITE (2) ----------------------------CNMP_BINDING_1   ------------------------CNMP_BINDING_2     ------------------------------------------------------------------------------HTH_CRP_1  PDB: A:167-19------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hw5 A   1 VLGKPQTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVLAEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVVYGT 208
                                    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:205
 aligned with CRP_ECOLI | P0ACJ8 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     
            CRP_ECOLI     2 VLGKPQTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVTSEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVV 206
               SCOP domains d1hw5b2 B:1-137 Catabolite gene activator protein, N-terminal domain                                                                     d1hw5b1 B:138-205                                                    SCOP domains
               CATH domains --------1hw5B01 B:9-137 Jelly Rolls                                                                                                      1hw5B02 B:138-205 'winged helix' repressor DNA binding domain        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh.eeeee....eee.......eeeeeee.eeeeeee.....eeeeeeee...eehhhhh.........eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee..eeee..hhhhhhhhhh.hhhhhhhhhhhhhhh..eee...eee. 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
                 1hw5 B   1 VLGKPQTDPTLEWFLSHCHIHKYPSKSTLIHQGEKAETLYYIVKGSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMRLSAQMARRLQVLAEKVGNLAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISAHGKTIVV 205
                                    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 '\|'

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. Organism_taxid: 562. (11)

1a	1hw5A02	A:138-205
1b	1hw5B02	B:138-205

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Jelly Rolls (177)

Escherichia coli. Organism_taxid: 562. (3)

2a	1hw5A01	A:9-137
2b	1hw5B01	B:9-137

(no "Pfam Domain" information available for 1HW5)

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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1g6n	CATABOLITE GENE ACTIVATOR PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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)

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Gene Ontology (12, 12)

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