Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL MECHANISM FOR THE FINE-TUNING OF CCPA FUNCTION BY THE SMALL MOLECULE EFFECTORS GLUCOSE-6-PHOSPHATE AND FRUCTOSE-1,6-BISPHOSPHATE
 
Authors :  M. A. Schumacher, G. Seidel, W. Hillen, R. G. Brennan
Date :  30 Dec 06  (Deposition) - 01 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.17
Chains :  Asym. Unit :  G,L
Biol. Unit 1:  G,L  (2x)
Keywords :  Ccpa, Ccr, Hpr, Crh, Protein-Dna, Adjunct Corepressor, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Schumacher, G. Seidel, W. Hillen, R. G. Brennan
Structural Mechanism For The Fine-Tuning Of Ccpa Function By The Small Molecule Effectors Glucose 6-Phosphate And Fructose 1, 6-Bisphosphate.
J. Mol. Biol. V. 368 1042 2007
PubMed-ID: 17376479  |  Reference-DOI: 10.1016/J.JMB.2007.02.054
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CATABOLITE CONTROL PROTEIN
    ChainsG
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentDELTA CCPA (RESIDUES 53-332)
    GeneCCPA
    Organism ScientificBACILLUS MEGATERIUM
    Organism Taxid1404
 
Molecule 2 - PHOSPHOCARRIER PROTEIN HPR
    ChainsL
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePTSH
    Organism ScientificBACILLUS MEGATERIUM
    Organism Taxid1404
    SynonymHISTIDINE-CONTAINING PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit GL
Biological Unit 1 (2x)GL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SEP1Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SEP2Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (0, 0)

(no "Site" information available for 2OEN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PTS_HPR_HISPS00369 PTS HPR domain histidine phosphorylation site signature.PTHP_BACME13-20  1L:13-20
2PTS_HPR_SERPS00589 PTS HPR domain serine phosphorylation site signature.PTHP_BACME39-54  1L:39-54
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PTS_HPR_HISPS00369 PTS HPR domain histidine phosphorylation site signature.PTHP_BACME13-20  2L:13-20
2PTS_HPR_SERPS00589 PTS HPR domain serine phosphorylation site signature.PTHP_BACME39-54  2L:39-54

(-) Exons   (0, 0)

(no "Exon" information available for 2OEN)

(-) 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 G from PDB  Type:PROTEIN  Length:275
 aligned with CCPA_BACME | P46828 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:275
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327     
           CCPA_BACME    58 KKTTTVGVIIPDISNIFYAELARGIEDIATMYKYNIILSNSDQNQDKELHLLNNMLGKQVDGIIFMSGNVTEEHVEELKKSPVPVVLAASIESTNQIPSVTIDYEQAAFDAVQSLIDSGHKNIAFVSGTLEEPINHAKKVKGYKRALTESGLPVRDSYIVEGDYTYDSGIEAVEKLLEEDEKPTAIFVGTDEMALGVIHGAQDRGLNVPNDLEIIGFDNTRLSTMVRPQLTSVVQPMYDIGAVAMRLLTKYMNKETVDSSIVQLPHRIEFRQSTK 332
               SCOP domains d2oeng_ G: Glucose-resistance amylase regulator CcpA, C-terminal domain                                                                                                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------Peripla_BP_3-2oenG01 G:169-331                                                                                                                                     - Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhh....eee.....hhhhhhhhhhh.................eeeehhhhhhhhhhhhhhh.......ee...........hhhhhhhhhhhh.........ee....hhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhh..........ee.eee.hhhhh.......eee.hhhhhhhhhhhhhhhhhh.......eeee..eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oen G  58 KKTTTVGVIIPDISNIFYAELARGIEDIATMYKYNIILSNSDQNQDKELHLLNNMLGKQVDGIIFMSGNVTEEHVEELKKSPVPVVLAASIESTNQIPSVTIDYEQAAFDAVQSLIDSGHKNIAFVSGTLEEPINHAKKVKGYKRALTESGLPVRDSYIVEGDYTYDSGIEAVEKLLEEDEKPTAIFVGTDEMALGVIHGAQDRGLNVPNDLEIIGFDNTRLSTMVRPQLTSVVQPMYDIGAVAMRLLTKYMNKETVDSSIVQLPHRIEFRQSTK 332
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327     

Chain L from PDB  Type:PROTEIN  Length:87
 aligned with PTHP_BACME | O69250 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:87
                                    11        21        31        41        51        61        71        81       
           PTHP_BACME     2 AQKTFTVTADSGIHARPATTLVQAASKFDSDINLEFNGKTVNLKSIMGVMSLGIQKGATITISAEGSDEADALAALEDTMSKEGLGE  88
               SCOP domains d2oenl_ L: Histidine-containing phosphocarrier protein (HPr)                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains PTS-HPr-2oenL01 L:2-84                                                             ---- Pfam domains
         Sec.struct. author ....ee.......hhhhhhhhhhhhhh......eee...ee....hhhhhhh......eeee.....hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PTS_HPR_------------------PTS_HPR_SER     ---------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 2oen L   2 AQKTFTVTADSGIHARPATTLVQAASKFDSDINLEFNGKTVNLKsIMGVMSLGIQKGATITISAEGSDEADALAALEDTMSKEGLGE  88
                                    11        21        31        41    |   51        61        71        81       
                                                                       46-SEP                                      

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit

(-) Gene Ontology  (13, 15)

Asymmetric Unit(hide GO term definitions)
Chain G   (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.

Chain L   (PTHP_BACME | O69250)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0008643    carbohydrate transport    The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y.
    GO:0009401    phosphoenolpyruvate-dependent sugar phosphotransferase system    The uptake and phosphorylation of specific carbohydrates from the extracellular environment; uptake and phosphorylation are coupled, making the PTS a link between the uptake and metabolism of sugars; phosphoenolpyruvate is the original phosphate donor; phosphoenolpyruvate passes the phosphate via a signal transduction pathway, to enzyme 1 (E1), which in turn passes it on to the histidine protein, HPr; the next step in the system involves sugar-specific membrane-bound complex, enzyme 2 (EII), which transports the sugar into the cell; it includes the sugar permease, which catalyzes the transport reactions; EII is usually divided into three different domains, EIIA, EIIB, and EIIC.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    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.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    SEP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2oen)
 
  Cis Peptide Bonds
    Arg G:284 - Pro G:285   [ RasMol ]  
    Val G:265 - Pro G:266   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2oen
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CCPA_BACME | P46828
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  PTHP_BACME | O69250
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CCPA_BACME | P46828
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PTHP_BACME | O69250
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CCPA_BACME | P468281rzr 1sxg 1sxh 1sxi 1zvv 2hsg 2jcg 2nzu 2nzv
        PTHP_BACME | O692501rzr 2nzu 2nzv

(-) Related Entries Specified in the PDB File

2nzu DELTA(CCPA)-HPR-SER46P-G6P
2nzv DELTA(CCPA)-HPRSER46P-FBP