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(-) Description

Title :  STRUCTURE OF CCPA-HPR-SER46P-ACKA2 COMPLEX
 
Authors :  M. A. Schumacher, M. Sprehe, M. Bartholomae, W. Hillen, R. G. Brennan
Date :  03 Sep 10  (Deposition) - 08 Dec 10  (Release) - 27 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.96
Chains :  Asym./Biol. Unit :  A,B,C,D,E,S
Keywords :  Pbp Fold For Ccpa, Transcription, Hpr-Ser46-P And Cre Dna, Nucleoid, Transcription-Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Schumacher, M. Sprehe, M. Bartholomae, W. Hillen, R. G. Brennan
Structures Of Carbon Catabolite Protein A-(Hpr-Ser46-P) Bound To Diverse Catabolite Response Element Sites Reveal The Basis For High-Affinity Binding To Degenerate Dna Operators.
Nucleic Acids Res. V. 39 2931 2011
PubMed-ID: 21106498  |  Reference-DOI: 10.1093/NAR/GKQ1177

(-) Compounds

Molecule 1 - CATABOLITE CONTROL PROTEIN A
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ALSA, AMYR, BSU29740, CCPA, GRAR
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: GLUCOSE-RESISTANCE AMYLASE REGULATOR
 
Molecule 2 - PHOSPHOCARRIER PROTEIN HPR
    Chains: S, D
    EC Number: 2.7.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BSU13900, HPR, PTSH
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: HISTIDINE-CONTAINING PROTEIN
 
Molecule 3 - 5'-D(*TP*TP*GP*TP*AP*AP*GP*CP*GP*TP*TP*AP*TP*CP*AP*A)-3'
    Chains: E
    Engineered: YES
 
Molecule 4 - 5'-D(*TP*TP*GP*AP*TP*AP*AP*CP*GP*CP*TP*TP*AP*CP*AP*A)-3'
    Chains: B
    Engineered: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDES

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1SEP2Mod. Amino AcidPHOSPHOSERINE
2SO44Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR C:90 , ARG C:304 , ASN C:311 , GLU C:313BINDING SITE FOR RESIDUE SO4 C 599
2AC2SOFTWARETYR A:90 , ARG A:304 , THR A:307 , ASN A:311 , GLU A:313BINDING SITE FOR RESIDUE SO4 A 499
3AC3SOFTWAREMET A:89 , TYR A:90BINDING SITE FOR RESIDUE SO4 A 399

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ile A:266 -Pro A:267
2Arg A:285 -Pro A:286
3Ile C:266 -Pro C:267
4Arg C:285 -Pro C:286

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (4, 8)

Asymmetric/Biological Unit (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LACI_2PS50932 LacI-type HTH domain profile.CCPA_BACSU4-58
 		  2A:4-58
C:4-58
2HTH_LACI_1PS00356 LacI-type HTH domain signature.CCPA_BACSU6-24
 		  2A:6-24
C:6-24
3PTS_HPR_HISPS00369 PTS HPR domain histidine phosphorylation site signature.PTHP_BACSU13-20
 		  2D:13-20
S:13-20
4PTS_HPR_SERPS00589 PTS HPR domain serine phosphorylation site signature.PTHP_BACSU39-54
 		  2D:39-54
S:39-54

(-) Exons   (0, 0)

(no "Exon" information available for 3OQM)

(-) 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:332
 aligned with CCPA_BACSU | P25144 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:332
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331  
           CCPA_BACSU     2 SNITIYDVAREANVSMATVSRVVNGNPNVKPTTRKKVLEAIERLGYRPNAVARGLASKKTTTVGVIIPDISSIFYSELARGIEDIATMYKYNIILSNSDQNMEKELHLLNTMLGKQVDGIVFMGGNITDEHVAEFKRSPVPIVLAASVEEQEETPSVAIDYEQAIYDAVKLLVDKGHTDIAFVSGPMAEPINRSKKLQGYKRALEEANLPFNEQFVAEGDYTYDSGLEALQHLMSLDKKPTAILSATDEMALGIIHAAQDQGLSIPEDLDIIGFDNTRLSLMVRPQLSTVVQPTYDIGAVAMRLLTKLMNKEPVEEHIVELPHRIELRKSTK 333
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh....eee.....hhhhhhhhhh....eeee..........eee.hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhh.....hhh.eee...hhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhh........eeeeee.hhhhhh.....eeee.hhhhhhhhhhhhhhhhhh.......eee...eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --HTH_LACI_2  PDB: A:4-58 UniProt: 4-58                  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----HTH_LACI_1         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oqm A   2 MNITIYDVAREANVSMATVSRVVNGNPNVKPTTRKKVLEAIERLGYRPNAVARGLASKKTTTVGVIIPDISSIFYSELARGIEDIATMYKYNIILSNSDQNMEKELHLLNTMLGKQVDGIVFMGGNITDEHVAEFKRSPVPIVLAASVEEQEETPSVAIDYEQAIYDAVKLLVDKGHTDIAFVSGPMAEPINRSKKLQGYKRALEEANLPFNEQFVAEGDYTYDSGLEALQHLMSLDKKPTAILSATDEMALGIIHAAQDQGLSIPEDLDIIGFDNTRLSLMVRPQLSTVVQPTYDIGAVAMRLLTKLMNKEPVEEHIVELPHRIELRKSTK 333
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331  


Chain B from PDB  Type:DNA  Length:16
                                                
                 3oqm B 700 TTGATAACGCTTACAA 715
                                   709      


Chain C from PDB  Type:PROTEIN  Length:332
 aligned with CCPA_BACSU | P25144 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:332
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331  
           CCPA_BACSU     2 SNITIYDVAREANVSMATVSRVVNGNPNVKPTTRKKVLEAIERLGYRPNAVARGLASKKTTTVGVIIPDISSIFYSELARGIEDIATMYKYNIILSNSDQNMEKELHLLNTMLGKQVDGIVFMGGNITDEHVAEFKRSPVPIVLAASVEEQEETPSVAIDYEQAIYDAVKLLVDKGHTDIAFVSGPMAEPINRSKKLQGYKRALEEANLPFNEQFVAEGDYTYDSGLEALQHLMSLDKKPTAILSATDEMALGIIHAAQDQGLSIPEDLDIIGFDNTRLSLMVRPQLSTVVQPTYDIGAVAMRLLTKLMNKEPVEEHIVELPHRIELRKSTK 333
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---LacI-3oqmC01 C:5-50                           --------------------------------------------------------------------------------------------------------Peripla_BP_3-3oqmC03 C:155-332                                                                                                                                                    - Pfam domains (1)
           Pfam domains (2) ---LacI-3oqmC02 C:5-50                           --------------------------------------------------------------------------------------------------------Peripla_BP_3-3oqmC04 C:155-332                                                                                                                                                    - Pfam domains (2)
         Sec.struct. author ...hhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhh....eeee..........eee.hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhh.........eee...hhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhh.........eeeeee.hhhhhh.....eeee.hhhhhhhhhhhhhhhhhh.......eee....ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --HTH_LACI_2  PDB: C:4-58 UniProt: 4-58                  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----HTH_LACI_1         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oqm C   2 MNITIYDVAREANVSMATVSRVVNGNPNVKPTTRKKVLEAIERLGYRPNAVARGLASKKTTTVGVIIPDISSIFYSELARGIEDIATMYKYNIILSNSDQNMEKELHLLNTMLGKQVDGIVFMGGNITDEHVAEFKRSPVPIVLAASVEEQEETPSVAIDYEQAIYDAVKLLVDKGHTDIAFVSGPMAEPINRSKKLQGYKRALEEANLPFNEQFVAEGDYTYDSGLEALQHLMSLDKKPTAILSATDEMALGIIHAAQDQGLSIPEDLDIIGFDNTRLSLMVRPQLSTVVQPTYDIGAVAMRLLTKLMNKEPVEEHIVELPHRIELRKSTK 333
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331  


Chain D from PDB  Type:PROTEIN  Length:87
 aligned with PTHP_BACSU | P08877 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:87
                                    11        21        31        41        51        61        71        81       
           PTHP_BACSU     2 AQKTFKVTADSGIHARPATVLVQTASKYDADVNLEYNGKTVNLKSIMGVMSLGIAKGAEITISASGADENDALNALEETMKSEGLGE  88
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.......hhhhhhhhhhhhh......eee....eee..hhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------PTS_HPR_SER     ---------------------------------- PROSITE (2)
                PROSITE (3) -----------PTS_HPR_-------------------------------------------------------------------- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3oqm D   2 AQKTFKVTADSGIHARPATVLVQTASKYDADVNLEYNGKTVNLKsIMGVMSLGIAKGAEITISASGADENDALNALEETMKSEGLGE  88
                                    11        21        31        41    |   51        61        71        81       
                                                                       46-SEP                                      


Chain E from PDB  Type:DNA  Length:16
                                                
                 3oqm E 700 TTGTAAGCGTTATCAA 715
                                   709      


Chain S from PDB  Type:PROTEIN  Length:87
 aligned with PTHP_BACSU | P08877 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:87
                                    11        21        31        41        51        61        71        81       
           PTHP_BACSU     2 AQKTFKVTADSGIHARPATVLVQTASKYDADVNLEYNGKTVNLKSIMGVMSLGIAKGAEITISASGADENDALNALEETMKSEGLGE  88
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) PTS-HPr-3oqmS01 S:2-84                                                             ---- Pfam domains (1)
           Pfam domains (2) PTS-HPr-3oqmS02 S:2-84                                                             ---- Pfam domains (2)
         Sec.struct. author ...eee.......hhhhhhhhhhhhhh...eeeeee..eeee..hhhhhhhh......eeeeeee..hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------PTS_HPR_SER     ---------------------------------- PROSITE (2)
                PROSITE (3) -----------PTS_HPR_-------------------------------------------------------------------- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3oqm S   2 AQKTFKVTADSGIHARPATVLVQTASKYDADVNLEYNGKTVNLKsIMGVMSLGIAKGAEITISASGADENDALNALEETMKSEGLGE  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  (0, 0)

(no "SCOP Domain" information available for 3OQM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)
(-)
Clan: Periplas_BP (97)
(-)
Clan: no clan defined [family: PTS-HPr] (26)

(-) Gene Ontology  (15, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (CCPA_BACSU | P25144)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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 D,S   (PTHP_BACSU | P08877)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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: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:0043610    regulation of carbohydrate utilization    Any process that modulates the frequency, rate or extent of carbohydrate utilization.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CCPA_BACSU | P25144: 1zvv 2fep 3oqn 3oqo
        PTHP_BACSU | P08877: 1jem 1kkl 1kkm 1sph 2fep 2hid 2hpr 3oqn 3oqo

(-) Related Entries Specified in the PDB File

3oqn 3oqo