3H3U - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CRP (CAMP RECEPTOR PROTEIN) FROM MYCOBACTERIUM TUBERCULOSIS

Authors :   P. Kumar, D. C. Joshi, M. Akif, Y. Akhter, S. E. Hasnain, S. C. Mande

Date :   17 Apr 09 (Deposition) - 02 Feb 10 (Release) - 05 May 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Apo Crp, Allostery, Dimer, Dna-Binding, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Kumar, D. C. Joshi, M. Akif, Y. Akhter, S. E. Hasnain, S. C. Mande
Mapping Conformational Transitions In Cyclic Amp Receptor Protein: Crystal Structure And Normal-Mode Analysis Of Mycobacterium Tuberculosis Apo-Camp Receptor Protein
Biophys. J. V. 98 305 2010
PubMed-ID: 20338852 | Reference-DOI: 10.1016/J.BPJ.2009.10.016

Molecule 1 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY CRP/FNR-FAMILY)
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A(+)
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RV3676
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	CRP, TRANSCRIPTIONAL REGULATOR, CRP/FNR FAMILY

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CMP	1	Ligand/Ion	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:79 , LEU A:81 , SER A:82 , ARG A:89 , THR A:90 , SER A:91 , HOH A:230 , ARG B:132	BINDING SITE FOR RESIDUE SO4 A 225
2	AC2	SOFTWARE	ARG A:132 , GLY B:79 , LEU B:81 , SER B:82 , ARG B:89 , THR B:90	BINDING SITE FOR RESIDUE SO4 B 225
3	AC3	SOFTWARE	ALA A:114 , GLY A:166 , GLY A:167 , MET B:1 , ASP B:2 , ALA B:114 , ASP B:115 , PRO B:117	BINDING SITE FOR RESIDUE CMP B 226

(no "SS Bond" information available for 3H3U)

(no "Cis Peptide Bond" information available for 3H3U)

(no "SAP(SNP)/Variant" information available for 3H3U)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	CRPL_MYCTO	10-130	2	A:10-130 B:10-130
1	CNMP_BINDING_3	PS50042	cAMP/cGMP binding motif profile.	CRPL_MYCTU	10-130	2	A:10-130 B:10-130
2	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	CRPL_MYCTO	144-217	2	A:144-217 B:144-214
2	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	CRPL_MYCTU	144-217	2	A:144-217 B:144-214

(no "Exon" information available for 3H3U)

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:216
 aligned with CRPL_MYCTO | P9WMH2 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221   
           CRPL_MYCTO     2 DEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISDSERLARRAR 224
               SCOP domains d3h3ua1 A:2-    144 au   tomated matches                                                                                                       d3h3ua2 A:145-224 automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.....----hhhhhh---.eeee....eee....ee.eeeeeee..eeeeee.....eeeeeee....ee.hhhhhh.ee...eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee..eeeee...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------CNMP_BINDING_3  PDB: A:10-130 UniProt: 10-130                                                                            -------------HTH_CRP_2  PDB: A:144-217 UniProt: 144-217                                ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h3u A   2 DEILARAGIFQG----AIAALT---QPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISDSERLARRAR 224
                                    11 |    | 21 |   |  31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221   
                                      13   18   23  27

Chain A from PDB  Type:PROTEIN  Length:216
 aligned with CRPL_MYCTU | P9WMH3 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221   
           CRPL_MYCTU     2 DEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISDSERLARRAR 224
               SCOP domains d3h3ua1 A:2-    144 au   tomated matches                                                                                                       d3h3ua2 A:145-224 automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.....----hhhhhh---.eeee....eee....ee.eeeeeee..eeeeee.....eeeeeee....ee.hhhhhh.ee...eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee..eeeee...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------CNMP_BINDING_3  PDB: A:10-130 UniProt: 10-130                                                                            -------------HTH_CRP_2  PDB: A:144-217 UniProt: 144-217                                ------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h3u A   2 DEILARAGIFQG----AIAALT---QPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISDSERLARRAR 224
                                    11 |    | 21 |   |  31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221   
                                      13   18   23  27

Chain B from PDB  Type:PROTEIN  Length:214
 aligned with CRPL_MYCTO | P9WMH2 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    
           CRPL_MYCTO     1 MDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLIS 214
               SCOP domains d3h3ub1 B:1-144 automated matches                                                                                                               d3h3ub2 B:145-214 automated matches                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..hhhhhhhhhh....eee....eee....ee.eeeeeee..eeeeee.....eeeeeee....eehhhhhh..ee...eeee...eeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhee....eeee...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------CNMP_BINDING_3  PDB: B:10-130 UniProt: 10-130                                                                            -------------HTH_CRP_2  PDB: B:144-214 UniProt: 144-217                              PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h3u B   1 MDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLIS 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:214
 aligned with CRPL_MYCTU | P9WMH3 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    
           CRPL_MYCTU     1 MDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLIS 214
               SCOP domains d3h3ub1 B:1-144 automated matches                                                                                                               d3h3ub2 B:145-214 automated matches                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..hhhhhhhhhh....eee....eee....ee.eeeeeee..eeeeee.....eeeeeee....eehhhhhh..ee...eeee...eeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhee....eeee...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------CNMP_BINDING_3  PDB: B:10-130 UniProt: 10-130                                                                            -------------HTH_CRP_2  PDB: B:144-214 UniProt: 144-217                              PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h3u B   1 MDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLIS 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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)

Mycobacterium tuberculosis [TaxId: 83332] (3)

1a	d3h3ua2	A:145-224
1b	d3h3ub2	B:145-214

Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: cAMP-binding domain-like (99)

Family: automated matches (17)

Protein domain: automated matches (17)

Mycobacterium tuberculosis [TaxId: 83332] (2)

2a	d3h3ua1	A:2-144
2b	d3h3ub1	B:1-144

(no "CATH Domain" information available for 3H3U)

(no "Pfam Domain" information available for 3H3U)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CRPL_MYCTU | P9WMH3)

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:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	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:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	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:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,B (CRPL_MYCTO | P9WMH2)

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.
biological process
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3h3u)

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	3h3u
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UniProtKB/Swiss-Prot
	CRPL_MYCTO \| P9WMH2	:	3d0s 3i54 3i59 3mzh 4a2u
	CRPL_MYCTU \| P9WMH3	:	3d0s 3i54 3i59 3mzh 4a2u

1g6n	E.COLI CRP BOUND WITH CAMP
1o3t	E.COLI CRP BOUND WITH DNA AS WELL AS CAMP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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SCOP Domains (2, 4)

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Gene Ontology (13, 19)

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