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(-) Description

Title :  APO FORM OF THE CATABOLITE CONTROL PROTEIN A (CCPA) FROM BACILLUS MEGATERIUM, WITH THE DNA BINDING DOMAIN
 
Authors :  R. K. Singh, S. Panjikar, G. J. Palm, W. Hinrichs
Date :  22 Dec 06  (Deposition) - 06 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Megaterium, Dna-Binding, Transcription, Ccpa, Bacillus, Apo- Form, Activator, Repressor, Transcription Regulation, Catabolite Control Protein A (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. K. Singh, G. J. Palm, S. Panjikar, W. Hinrichs
Structure Of The Apo Form Of The Catabolite Control Protein A (Ccpa) From Bacillus Megaterium With A Dna-Binding Domain.
Acta Crystallogr. , Sect. F V. 63 253 2007
PubMed-ID: 17401189  |  Reference-DOI: 10.1107/S1744309107008949
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCOSE-RESISTANCE AMYLASE REGULATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS MEGATERIUM
    Organism Taxid: 1404
    Synonym: CATABOLITE CONTROL PROTEIN, CATABOLITE CONTROL PROTEIN A

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:231 , GLU A:235BINDING SITE FOR RESIDUE CA A1333

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JCG)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:265 -Pro A:266
2Arg A:284 -Pro A:285

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JCG)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LACI_2PS50932 LacI-type HTH domain profile.CCPA_BACME3-57  1A:3-51
2HTH_LACI_1PS00356 LacI-type HTH domain signature.CCPA_BACME5-23  1A:5-23
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LACI_2PS50932 LacI-type HTH domain profile.CCPA_BACME3-57  2A:3-51
2HTH_LACI_1PS00356 LacI-type HTH domain signature.CCPA_BACME5-23  2A:5-23

(-) Exons   (0, 0)

(no "Exon" information available for 2JCG)

(-) Sequences/Alignments

Asymmetric 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:322
 aligned with CCPA_BACME | P46828 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:330
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
           CCPA_BACME     3 VTIYDVAREASVSMATVSRVVNGNPNVKPSTRKKVLETIERLGYRPNAVARGLASKKTTTVGVIIPDISNIFYAELARGIEDIATMYKYNIILSNSDQNQDKELHLLNNMLGKQVDGIIFMSGNVTEEHVEELKKSPVPVVLAASIESTNQIPSVTIDYEQAAFDAVQSLIDSGHKNIAFVSGTLEEPINHAKKVKGYKRALTESGLPVRDSYIVEGDYTYDSGIEAVEKLLEEDEKPTAIFVGTDEMALGVIHGAQDRGLNVPNDLEIIGFDNTRLSTMVRPQLTSVVQPMYDIGAVAMRLLTKYMNKETVDSSIVQLPHRIEFRQSTK 332
               SCOP domains d2jcga1 A:3-51                                   --------d2jcga2 A:60-332 Glucose-resistance amylase regulator CcpA, C-terminal domain                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -LacI-2jcgA01 A:4-49                           -----------------------------------------------------------------------------------------------------------------------Peripla_BP_3-2jcgA02 A:169-331                                                                                                                                     - Pfam domains
         Sec.struct. author .hhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhh......--------..eeeeee.........hhhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhh....eeee.....hhhhhhhhh.....eeee..........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhh.....hhh.eee...hhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh........eeeee..hhhhhh.....eeee.hhhhhhhhhhhhhhhhhh.......eeee..eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) HTH_LACI_2  PDB: A:3-51 UniProt: 3-57                  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --HTH_LACI_1         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2jcg A   3 VTIYDVAREASVSMATVSRVVNGNPNVKPSTRKKVLETIERLGYRPNAV--------TTTVGVIIPDISNIFYAELARGIEDIASMYKYNIILSNSDQNQDKQLHLLNNMLGKQVDGIIFMSGNVTEEHVEELKKSPVPVVLAASIESTNQIPSVTIDYEQAAFDAVQSLIDSGHKNIAFVSGTLEEPINHAKKVKGYKRALTESGLPVRDSYIVEGDYTYDSGIEAVEKLLEEDEKPTAIFVGTDEMALGVIHGAQDRGLNVPNDLEIIGFDNTRLSTMVRPQLTSVVQPMYDIGAVAMRLLTKYMNKETVDSSIVELPHRIEFRQSTK 332
                                    12        22        32        42        |-       |62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
                                                                           51       60
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JCG)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Clan: Periplas_BP (97)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (CCPA_BACME | P46828)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CCPA_BACME | P46828: 1rzr 1sxg 1sxh 1sxi 1zvv 2hsg 2nzu 2nzv 2oen

(-) Related Entries Specified in the PDB File

1rzr CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR- PHOSPHOPROTEIN-DNA COMPLEX
1sxg STRUCTURAL STUDIES ON THE APO TRANSCRIPTION FACTOR FORM B.MEGATERIUM
1sxh APO STRUCTURE OF B. MEGATERIUM TRANSCRIPTION REGULATOR
1sxi STRUCTURE OF APO TRANSCRIPTION REGULATOR B. MEGATERIUM
1zvv CRYSTAL STRUCTURE OF A CCPA-CRH-DNA COMPLEX