3I59 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF MTBCRP IN COMPLEX WITH N6-CAMP

Authors :   M. C. Reddy, S. K. Palaninathan, J. B. Bruning, C. Thurman, D. Smith, J. C. Sacchettini, Tb Structural Genomics Consortium (Tbsgc)

Date :   03 Jul 09 (Deposition) - 08 Sep 09 (Release) - 29 Dec 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.29

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

Keywords :   Mycobacterium Tuberculosis, Camp Receptor Protein, Crp, Allosteric Mechanism, Dna Binding, Inhibition, N6-Camp, Structural Genomics, Tb Structural Genomics Consortium, Tbsgc, Dna-Binding, Transcription, Transcription Regulation, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. C. Reddy, S. K. Palaninathan, J. B. Bruning, C. Thurman, D. Smith, J. C. Sacchettini
Structural Insights Into The Mechanism Of The Allosteric Transitions Of Mycobacterium Tuberculosis Camp Receptor Protein.
J. Biol. Chem. V. 284 36581 2009
PubMed-ID: 19740754 | Reference-DOI: 10.1074/JBC.M109.041343
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTIONAL REGULATOR, CRP/FNR FAMILY
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MT3777, RV3676
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773

Molecule 2 - TRANSCRIPTIONAL REGULATOR, CRP/FNR FAMILY
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MT3777, RV3676
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 4)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
3	N6R	1	Ligand/Ion	(2R)-N6-(1-METHYL-2-PHENYLETHYL)ADENOSINE-3',5'-CYCLICMONOPHOSPHATE
4	N6S	1	Ligand/Ion	(2S)-N6-(1-METHYL-2-PHENYLETHYL)ADENOSINE-3',5'-CYCLICMONOPHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:38 , ILE A:57 , LEU A:69 , PHE A:78 , GLY A:79 , GLU A:80 , LEU A:81 , SER A:82 , ARG A:89 , THR A:90 , SER A:91 , ARG A:130 , THR A:134 , ASN A:137 , LEU A:141 , ASN B:135	BINDING SITE FOR RESIDUE N6R A 301
2	AC2	SOFTWARE	ARG A:129 , ARG A:130 , ARG A:133 , ARG A:160	BINDING SITE FOR RESIDUE CL A 302
3	AC3	SOFTWARE	ASN A:135 , LEU A:138 , PHE B:38 , ILE B:57 , LEU B:69 , THR B:70 , PHE B:78 , GLY B:79 , GLU B:80 , LEU B:81 , SER B:82 , ARG B:89 , THR B:90 , SER B:91 , THR B:134	BINDING SITE FOR RESIDUE N6S B 301

(no "SS Bond" information available for 3I59)

(no "Cis Peptide Bond" information available for 3I59)

(no "SAP(SNP)/Variant" information available for 3I59)

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:145-215
2	HTH_CRP_2	PS51063	Crp-type HTH domain profile.	CRPL_MYCTU	144-217	2	A:144-217 B:145-215

(no "Exon" information available for 3I59)

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:215
 aligned with CRPL_MYCTO | P9WMH2 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:224
                             1                                                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
           CRPL_MYCTO     - -MDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISDSERLARRA 223
               SCOP domains d3i59a1 A:0-144 au       tomated matches                                                                                                         d3i59a2 A:145-223 automated matches                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.....-------....eee....eee.......eeeeeee..eeeee....--.eeeeee....ee.hhhhhh......eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee....eeee...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.hhhhhhhhh 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
                 3i59 A   0 HMDEILARAGIFQGVEPS-------QLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPD--ENLLTImGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISDSERLARRA 223
                                     9       | -     |  29        39        49        59   |  | 69  |     79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
                                            17      25                                    63 66     |                                                                                                                                                       
                                                                                                   72-MSE

Chain A from PDB  Type:PROTEIN  Length:215
 aligned with CRPL_MYCTU | P9WMH3 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:224
                             1                                                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
           CRPL_MYCTU     - -MDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISDSERLARRA 223
               SCOP domains d3i59a1 A:0-144 au       tomated matches                                                                                                         d3i59a2 A:145-223 automated matches                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.....-------....eee....eee.......eeeeeee..eeeee....--.eeeeee....ee.hhhhhh......eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee....eeee...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.hhhhhhhhh 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
                 3i59 A   0 HMDEILARAGIFQGVEPS-------QLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPD--ENLLTImGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISDSERLARRA 223
                                     9       | -     |  29        39        49        59   |  | 69  |     79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
                                            17      25                                    63 66     |                                                                                                                                                       
                                                                                                   72-MSE

Chain B from PDB  Type:PROTEIN  Length:202
 aligned with CRPL_MYCTO | P9WMH2 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:217
                              1                                                                                                                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       
           CRPL_MYCTO     - --MDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISD 215
               SCOP domains d3i59b1 B:-1-141        automated matches                                                                                                         d3i59b2 B:145-215 a     utomated matches                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...-------.....eeee....eee........eeeeee..eeeeee.....eeeeeee....ee.hhhhhh......eeee...eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....---.hhhhhhhhhhhhhhhhh.-----.......hhhhhhhhhh.hhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------CNMP_BINDING_3  PDB: B:10-130 UniProt: 10-130                                                                            -------------HTH_CRP_2  PDB: B:145-215 UniProt: 144-217                               PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i59 B  -1 SHMDEILARAGIFQGVE-------TKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADL---DVPGRVAKQLLQLAQRFGT-----LRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISD 215
                                     8      |  -    |   28        38        48        58        68        78        88        98       108       118       128       138  |   |148       158    |    -|      178       188       198       208       
                                           15      23                                                                                                                   141 145               163   169

Chain B from PDB  Type:PROTEIN  Length:202
 aligned with CRPL_MYCTU | P9WMH3 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:217
                              1                                                                                                                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       
           CRPL_MYCTU     - --MDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISD 215
               SCOP domains d3i59b1 B:-1-141        automated matches                                                                                                         d3i59b2 B:145-215 a     utomated matches                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...-------.....eeee....eee........eeeeee..eeeeee.....eeeeeee....ee.hhhhhh......eeee...eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....---.hhhhhhhhhhhhhhhhh.-----.......hhhhhhhhhh.hhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------CNMP_BINDING_3  PDB: B:10-130 UniProt: 10-130                                                                            -------------HTH_CRP_2  PDB: B:145-215 UniProt: 144-217                               PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i59 B  -1 SHMDEILARAGIFQGVE-------TKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADL---DVPGRVAKQLLQLAQRFGT-----LRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISD 215
                                     8      |  -    |   28        38        48        58        68        78        88        98       108       118       128       138  |   |148       158    |    -|      178       188       198       208       
                                           15      23                                                                                                                   141 145               163   169

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: 1773] (6)

1a	d3i59a2	A:145-223
1b	d3i59b2	B:145-215

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: 1773] (4)

2a	d3i59a1	A:0-144
2b	d3i59b1	B:-1-141

(no "CATH Domain" information available for 3I59)

(no "Pfam Domain" information available for 3I59)

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 3i59)

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	3i59
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	CRPL_MYCTO \| P9WMH2	:	3d0s 3h3u 3i54 3mzh 4a2u
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3i54	CRYSTAL STRUCTURE OF MTBCRP IN COMPLEX WITH CAMP RELATED ID: RV3676 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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SCOP Domains (2, 4)

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Pfam Domains (0, 0)

Gene Ontology (13, 19)

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