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(-) Description

Title :  PHOB EFFECTOR DOMAIN IN COMPLEX WITH PHO BOX DNA.
 
Authors :  A. G. Blanco, M. Sola, F. X. Gomis-Ruth, M. Coll
Date :  08 Apr 02  (Deposition) - 29 Apr 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Transcriptional Activator, Helix-Winged-Helix, Sensory Transduction, Phosphorylation, Dna Binding, Activator, Two- Component Signal Transduction (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. G. Blanco, M. Sola, F. X. Gomis-Ruth, M. Coll
Tandem Dna Recognition By Two-Component Signal Transduction Transcriptional Activator Phob
Structure V. 10 701 2002
PubMed-ID: 12015152  |  Reference-DOI: 10.1016/S0969-2126(02)00761-X

(-) Compounds

Molecule 1 - PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN
    ChainsA, B, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPBAT4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorESCHERICHIA COLI
    FragmentDNA-BINDING AND TRANSACTIVATION DOMAIN, RESIDUES 124-229
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsBOUND TO DNA, DNA CHAINS C, D, G, H
    Other Details - SourcePCR-CLONED DOMAIN FROM GENOMIC DNA
    SynonymPHOB
 
Molecule 2 - 5'-D(*GP*AP*GP*CP*TP*GP*TP*CP*AP*TP* AP*AP*AP*GP*TP*TP*GP*TP*CP*AP*CP*GP*G)-3'
    ChainsC, G
    SyntheticYES
 
Molecule 3 - 5'-D(*CP*CP*CP*GP*TP*GP*AP*CP*AP*AP* CP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*T)-3'
    ChainsD, H
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)ABCD    
Biological Unit 2 (1x)    EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1GXP)

(-) Sites  (0, 0)

(no "Site" information available for 1GXP)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GXP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GXP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GXP)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPR_PHOBPS51755 OmpR/PhoB-type DNA-binding domain profile.PHOB_ECO57129-227
 
 
 
  4A:129-227
B:129-227
E:129-227
F:129-227
PHOB_ECOLI129-227
 
 
 
  4A:129-227
B:129-227
E:129-227
F:129-227
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPR_PHOBPS51755 OmpR/PhoB-type DNA-binding domain profile.PHOB_ECO57129-227
 
 
 
  2A:129-227
B:129-227
-
-
PHOB_ECOLI129-227
 
 
 
  2A:129-227
B:129-227
-
-
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPR_PHOBPS51755 OmpR/PhoB-type DNA-binding domain profile.PHOB_ECO57129-227
 
 
 
  2-
-
E:129-227
F:129-227
PHOB_ECOLI129-227
 
 
 
  2-
-
E:129-227
F:129-227

(-) Exons   (0, 0)

(no "Exon" information available for 1GXP)

(-) 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:103
 aligned with PHOB_ECO57 | P0AFJ6 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:103
                                   136       146       156       166       176       186       196       206       216       226   
           PHOB_ECO57   127 AVEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
               SCOP domains d1gxpa_ A: PhoB                                                                                         SCOP domains
               CATH domains 1gxpA00 A:127-229 'winged helix' repressor DNA binding domain                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee....eeee..eee...hhhhhhhhhhhh...eee.hhhhhhhhh.......hhhhhhhhhhhhhhh....hhh.eeee...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --OMPR_PHOB  PDB: A:129-227 UniProt: 129-227                                                         -- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1gxp A 127 AVEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
                                   136       146       156       166       176       186       196       206       216       226   

Chain A from PDB  Type:PROTEIN  Length:103
 aligned with PHOB_ECOLI | P0AFJ5 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:103
                                   136       146       156       166       176       186       196       206       216       226   
           PHOB_ECOLI   127 AVEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
               SCOP domains d1gxpa_ A: PhoB                                                                                         SCOP domains
               CATH domains 1gxpA00 A:127-229 'winged helix' repressor DNA binding domain                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee....eeee..eee...hhhhhhhhhhhh...eee.hhhhhhhhh.......hhhhhhhhhhhhhhh....hhh.eeee...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --OMPR_PHOB  PDB: A:129-227 UniProt: 129-227                                                         -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1gxp A 127 AVEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
                                   136       146       156       166       176       186       196       206       216       226   

Chain B from PDB  Type:PROTEIN  Length:101
 aligned with PHOB_ECO57 | P0AFJ6 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:101
                                   138       148       158       168       178       188       198       208       218       228 
           PHOB_ECO57   129 EEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
               SCOP domains d1gxpb_ B: PhoB                                                                                       SCOP domains
               CATH domains 1gxpB00 B:129-229 'winged helix' repressor DNA binding domain                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee....eeee..eee...hhhhhhhhhhhh...eee.hhhhhhhhh.......hhhhhhhhhhhhhhh....hhh.eeee...eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) OMPR_PHOB  PDB: B:129-227 UniProt: 129-227                                                         -- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1gxp B 129 EEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
                                   138       148       158       168       178       188       198       208       218       228 

Chain B from PDB  Type:PROTEIN  Length:101
 aligned with PHOB_ECOLI | P0AFJ5 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:101
                                   138       148       158       168       178       188       198       208       218       228 
           PHOB_ECOLI   129 EEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
               SCOP domains d1gxpb_ B: PhoB                                                                                       SCOP domains
               CATH domains 1gxpB00 B:129-229 'winged helix' repressor DNA binding domain                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee....eeee..eee...hhhhhhhhhhhh...eee.hhhhhhhhh.......hhhhhhhhhhhhhhh....hhh.eeee...eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE OMPR_PHOB  PDB: B:129-227 UniProt: 129-227                                                         -- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1gxp B 129 EEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
                                   138       148       158       168       178       188       198       208       218       228 

Chain C from PDB  Type:DNA  Length:23
                                                       
                 1gxp C   1 GAGCTGTCATAAAGTTGTCACGG  23
                                    10        20   

Chain D from PDB  Type:DNA  Length:23
                                                       
                 1gxp D   1 CCCGTGACAACTTTATGACAGCT  23
                                    10        20   

Chain E from PDB  Type:PROTEIN  Length:102
 aligned with PHOB_ECO57 | P0AFJ6 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:102
                                   137       147       157       167       177       187       197       207       217       227  
           PHOB_ECO57   128 VEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
               SCOP domains d1gxpe_ E: PhoB                                                                                        SCOP domains
               CATH domains 1gxpE00 E:128-229 'winged helix' repressor DNA binding domain                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee....eeee..eee...hhhhhhhhhhhh...eee.hhhhhhhhh.......hhhhhhhhhhhhhhh....hhh.eeee...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -OMPR_PHOB  PDB: E:129-227 UniProt: 129-227                                                         -- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1gxp E 128 VEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
                                   137       147       157       167       177       187       197       207       217       227  

Chain E from PDB  Type:PROTEIN  Length:102
 aligned with PHOB_ECOLI | P0AFJ5 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:102
                                   137       147       157       167       177       187       197       207       217       227  
           PHOB_ECOLI   128 VEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
               SCOP domains d1gxpe_ E: PhoB                                                                                        SCOP domains
               CATH domains 1gxpE00 E:128-229 'winged helix' repressor DNA binding domain                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee....eeee..eee...hhhhhhhhhhhh...eee.hhhhhhhhh.......hhhhhhhhhhhhhhh....hhh.eeee...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -OMPR_PHOB  PDB: E:129-227 UniProt: 129-227                                                         -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1gxp E 128 VEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
                                   137       147       157       167       177       187       197       207       217       227  

Chain F from PDB  Type:PROTEIN  Length:102
 aligned with PHOB_ECO57 | P0AFJ6 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:102
                                   137       147       157       167       177       187       197       207       217       227  
           PHOB_ECO57   128 VEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
               SCOP domains d1gxpf_ F: PhoB                                                                                        SCOP domains
               CATH domains 1gxpF00 F:128-229 'winged helix' repressor DNA binding domain                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee....eeee..eee...hhhhhhhhhhhh...eee.hhhhhhhhh.......hhhhhhhhhhhhhhh....hhh.eeee...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -OMPR_PHOB  PDB: F:129-227 UniProt: 129-227                                                         -- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1gxp F 128 VEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
                                   137       147       157       167       177       187       197       207       217       227  

Chain F from PDB  Type:PROTEIN  Length:102
 aligned with PHOB_ECOLI | P0AFJ5 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:102
                                   137       147       157       167       177       187       197       207       217       227  
           PHOB_ECOLI   128 VEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
               SCOP domains d1gxpf_ F: PhoB                                                                                        SCOP domains
               CATH domains 1gxpF00 F:128-229 'winged helix' repressor DNA binding domain                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee....eeee..eee...hhhhhhhhhhhh...eee.hhhhhhhhh.......hhhhhhhhhhhhhhh....hhh.eeee...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -OMPR_PHOB  PDB: F:129-227 UniProt: 129-227                                                         -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1gxp F 128 VEEVIEMQGLSLDPTSHRVMAGEEPLEMGPTEFKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEPGGHDRMVQTVRGTGYRFSTRF 229
                                   137       147       157       167       177       187       197       207       217       227  

Chain G from PDB  Type:DNA  Length:23
                                                       
                 1gxp G   1 GAGCTGTCATAAAGTTGTCACGG  23
                                    10        20   

Chain H from PDB  Type:DNA  Length:23
                                                       
                 1gxp H   1 CCCGTGACAACTTTATGACAGCT  23
                                    10        20   

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GXP)

(-) Gene Ontology  (11, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B,E,F   (PHOB_ECO57 | P0AFJ6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000156    phosphorelay response regulator activity    Responds to a phosphorelay sensor to initiate a change in cell state or activity. The activity of the response regulator is regulated by transfer of a phosphate from a histidine residue in the sensor, to an aspartate residue in the response regulator. Many but not all response regulators act as transcriptional regulators to elicit a response.
biological process
    GO:0006817    phosphate ion transport    The directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    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.

Chain A,B,E,F   (PHOB_ECOLI | P0AFJ5)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0001108    bacterial-type RNA polymerase holo enzyme binding    Interacting selectively and non-covalently with the basal transcription machinery which is composed of a bacterial-type RNA polymerase core enzyme and a sigma factor, the minimal set of factors required for formation of the preinitiation complex (PIC) by a bacterial-type RNA polymerase.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000156    phosphorelay response regulator activity    Responds to a phosphorelay sensor to initiate a change in cell state or activity. The activity of the response regulator is regulated by transfer of a phosphate from a histidine residue in the sensor, to an aspartate residue in the response regulator. Many but not all response regulators act as transcriptional regulators to elicit a response.
biological process
    GO:0006817    phosphate ion transport    The directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    GO:2000142    regulation of DNA-templated transcription, initiation    Any process that modulates the frequency, rate or extent of DNA-templated transcription initiation.
    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
        PHOB_ECO57 | P0AFJ61b00 1qqi 1zes
        PHOB_ECOLI | P0AFJ51b00 1gxq 1qqi 1zes 2iyn 2jb9 2jba 2z33 3t72

(-) Related Entries Specified in the PDB File

1b00 PHOB RECEIVER DOMAIN FROM ESCHERICHIA COLI
1gxq CRYSTAL STRUCTURE OF THE PHOB EFFECTOR DOMAIN
1qqi SOLUTION STRUCTURE OF THE DEOXYRIBONUCLEIC ACID-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI