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(-) Description

Title :  CRYSTAL STRUCTURE OF CAMP RECEPTOR PROTEIN FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH CAMP AND ITS DNA BINDING ELEMENT
 
Authors :  Y. Akhter, M. Wilmanns
Date :  12 May 10  (Deposition) - 08 Jun 11  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transcription, Transcription Regulator, Camp, Camp Receptor Protein, Crp, Rv3676, Dna-Binding, Transcription Regulation, Transcription- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Akhter, V. Pogenberg, S. E. Hasnain, M. Wilmanns
Crystal Structure Of Camp Receptor Protein From Mycobacterium Tuberculosis In Complex With Dna And Camp
To Be Published
PubMed: search

(-) Compounds

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: BL21(DE3)
    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
 
Molecule 2 - 5'-D(P*AP*AP*AP*TP*GP*TP*GP*AP*TP*CP*TP*AP*GP*GP*TP*CP*AP*C P*GP*TP*G)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(P*CP*AP*CP*GP*TP*GP*AP*CP*CP*TP*AP*GP*AP*TP*CP*AP*CP*A P*TP*C)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1CMP3Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:38 , 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 , ARG B:132 , ASN B:135BINDING SITE FOR RESIDUE CMP A 623
2AC2SOFTWAREILE A:142 , ASN B:67 , LEU B:68 , LEU B:69 , ASN B:137 , ASP B:140 , LEU B:141 , ARG B:149 , LYS B:152 , GLN B:153 , GLN B:156 , GLN B:182 , LEU B:183 , VAL B:184 , GLY B:185BINDING SITE FOR RESIDUE CMP B 621
3AC3SOFTWARELEU A:131 , ASN A:135 , PHE B:38 , ILE B:57 , THR B:70 , PHE B:78 , GLY B:79 , GLU B:80 , LEU B:81 , SER B:82 , ARG B:89 , SER B:91 , ARG B:130 , ARG B:133 , THR B:134BINDING SITE FOR RESIDUE CMP B 622

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly B:13 -Val B:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.CRPL_MYCTO10-130
 		  2A:10-130
B:10-130
CRPL_MYCTU10-130
 		  2A:10-130
B:10-130
2HTH_CRP_2PS51063 Crp-type HTH domain profile.CRPL_MYCTO144-217
 		  2A:144-217
B:144-217
CRPL_MYCTU144-217
 		  2A:144-217
B:144-217

(-) Exons   (0, 0)

(no "Exon" information available for 3MZH)

(-) Sequences/Alignments

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:225
 aligned with CRPL_MYCTO | P9WMH2 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:225
                             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     - -MDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISDSERLARRAR 224
               SCOP domains d3mzha1 A:0-144 automated matches                                                                                                                d3mzha2 A:145-224 automated matches                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh........hhhhhhhhhhhh.eeee....eee.......eeeeeee..eeeeee.....eeeeeee....ee.hhhhhh......eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhheeee..eeee....hhhhhhhhh..hhhhhhhhhhhhhhh..eee....eee.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
                 3mzh A   0 HMDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISDSERLARRAR 224
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     


Chain A from PDB  Type:PROTEIN  Length:225
 aligned with CRPL_MYCTU | P9WMH3 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:225
                             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     - -MDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISDSERLARRAR 224
               SCOP domains d3mzha1 A:0-144 automated matches                                                                                                                d3mzha2 A:145-224 automated matches                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh........hhhhhhhhhhhh.eeee....eee.......eeeeeee..eeeeee.....eeeeeee....ee.hhhhhh......eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhheeee..eeee....hhhhhhhhh..hhhhhhhhhhhhhhh..eee....eee.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
                 3mzh A   0 HMDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISDSERLARRAR 224
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     


Chain B from PDB  Type:PROTEIN  Length:225
 aligned with CRPL_MYCTO | P9WMH2 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:225
                             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     - -MDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISDSERLARRAR 224
               SCOP domains d3mzhb1 B:0-144 automated matches                                                                                                                d3mzhb2 B:145-224 automated matches                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh......hhhhhhhhhhhh.eeee....eee.......eeeeeee..eeeeee.....eeeeeee....ee.hhhhhh......eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhheeee..eeee....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------CNMP_BINDING_3  PDB: B:10-130 UniProt: 10-130                                                                            -------------HTH_CRP_2  PDB: B:144-217 UniProt: 144-217                                ------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mzh B   0 HMDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISDSERLARRAR 224
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     


Chain B from PDB  Type:PROTEIN  Length:225
 aligned with CRPL_MYCTU | P9WMH3 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:225
                             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     - -MDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISDSERLARRAR 224
               SCOP domains d3mzhb1 B:0-144 automated matches                                                                                                                d3mzhb2 B:145-224 automated matches                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh......hhhhhhhhhhhh.eeee....eee.......eeeeeee..eeeeee.....eeeeeee....ee.hhhhhh......eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhheeee..eeee....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------CNMP_BINDING_3  PDB: B:10-130 UniProt: 10-130                                                                            -------------HTH_CRP_2  PDB: B:144-217 UniProt: 144-217                                ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mzh B   0 HMDEILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLLTIMGPSDMFGELSIFDPGPRTSSATTITEVRAVSMDRDALRSWIADRPEISEQLLRVLARRLRRTNNNLADLIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRLEGKSVLISDSERLARRAR 224
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219     


Chain C from PDB  Type:DNA  Length:21
                                                     
                 3mzh C   3 AAATGTGATCTAGGTCACGTG  23
                                    12        22 


Chain D from PDB  Type:DNA  Length:20
                                                    
                 3mzh D   3 CACGTGACCTAGATCACATC  22
                                    12        22
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 19)

Asymmetric/Biological Unit(hide GO term definitions)
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.

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.

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  3mzh
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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

(-) Related Entries Specified in the PDB File

3d0s APO-PROTEIN
3h3u APO-PROTEIN
3i54 CAMP BOUND
3i59 N6-CAMP BOUND