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(-) Description

Title :  PRFA, TRANSCRIPTIONAL REGULATOR IN LISTERIA MONOCYTOGENES
 
Authors :  M. Eiting, G. Hagelueken, W. -D. Schubert, D. W. Heinz
Date :  26 Nov 04  (Deposition) - 14 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription, Bacterial Infection, Human Pathogen, Transcriptional Regulator, Activator, Virulence (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Eiting, G. Hagelueken, W. -D. Schubert, D. W. Heinz
The Mutation G145S In Prfa, A Key Virulence Regulator Of Listeria Monocytogenes, Increases Dna-Binding Affinity By Stabilizing The Hth Motif
Mol. Microbiol. V. 56 433 2005
PubMed-ID: 15813735  |  Reference-DOI: 10.1111/J.1365-2958.2005.04561.X

(-) Compounds

Molecule 1 - LISTERIOLYSIN REGULATORY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-30
    Expression System Strain: M15
    Expression System Taxid: 562
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 169963
    Strain: EGD-E
    Synonym: PRFA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1ACM1Ligand/IonACETAMIDE
2CL2Ligand/IonCHLORIDE ION
3GLN1Mod. Amino AcidGLUTAMINE
4PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:61 , TYR A:62 , TYR A:126BINDING SITE FOR RESIDUE CL A1238
2AC2SOFTWAREGLN B:61 , TYR B:62 , TYR B:126BINDING SITE FOR RESIDUE CL B1238
3AC3SOFTWAREGLN A:61 , TYR A:62 , LYS A:64 , ALA A:66 , PHE A:67 , GLN A:123 , TYR A:126 , PG4 A:1239BINDING SITE FOR RESIDUE GLN A1240
4AC4SOFTWARETYR A:62 , TYR A:126 , GLN A:146 , LEU A:150 , GLN A:1240BINDING SITE FOR RESIDUE PG4 A1239
5AC5SOFTWAREGLN B:61 , TYR B:62 , GLN B:123 , TYR B:126BINDING SITE FOR RESIDUE ACM B1239

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:65 -Ala A:66
2Lys A:202 -Asn A:203
3Asn A:203 -Ser A:204

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PRFA_LISMO_001 *G145SPRFA_LISMO  ---  ---A/BG145S
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CRP_2PS51063 Crp-type HTH domain profile.PRFA_LISMO137-212
 		  2A:137-212
B:137-212
2HTH_CRP_1PS00042 Crp-type HTH domain signature.PRFA_LISMO169-193
 		  2A:169-193
B:169-193

(-) Exons   (0, 0)

(no "Exon" information available for 2BEO)

(-) 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:227
 aligned with PRFA_LISMO | P22262 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:237
                                                                                                                                                                                                                                                                     237 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231     | 
          PRFA_LISMO      2 NAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN-    -
               SCOP domains d2beoa2 A:2-137 automated matches                                                                                                       d2beoa1 A:138-237 automated matches                                                                 - SCOP domains
               CATH domains 2beoA01 A:2-109 Jelly Rolls                                                                                 ---------------------------2beoA02 A:137-237 'winged helix' repre          ssor DNA binding domain                              - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh....eeee...eee.......eeeeeee.eeeeeee.....eeeeeeee..eeee.............eeee...eeeeeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhheee....eee....hhhhhh----------hhhhhhhhhhh...eee....eee..hhhhhhh.hhhhhhhhhh.hhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------S--------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_2  PDB: A:137-212 UniProt: 137-212                                  -------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1  PDB: A:169-193--------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2beo A    2 NAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQEL----------AVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLNQ 1240
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171  |      -   |   191       201       211       221       231     ||
                                                                                                                                                                                                      174        185                                                 237|
                                                                                                                                                                                                                                                                     1240


Chain B from PDB  Type:PROTEIN  Length:231
 aligned with PRFA_LISMO | P22262 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:236
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      
          PRFA_LISMO      2 NAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN  237
               SCOP domains d2beob2 B:2-137 automated matches                                                                                                       d2beob1 B:138-237 automated matches                                                                  SCOP domains
               CATH domains 2beoB01 B:2-109 Jelly Rolls                                                                                 ---------------------------2beoB02 B:137-237 'winged helix' represso     r DNA binding domain                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh....eeee...eee.......eeeeeee.eeeeeee.....eeeeeeee..eeee.............eeee...eeeeeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhheee....eee....hhhhhh...-----.hhhhhhhhhhhh...eee....eee..hhhhhhh.hhhhhhhhhh.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------S-------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_2  PDB: B:137-212 UniProt: 137-212                                  ------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1  PDB: B:169-193-------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2beo B    2 NAQAEEFKKYLETNGIKPKQFHKKELIFNQWDPQEYCIFLYDGITKLTSISENGTIMNLQYYKGAFVIMSGFIDTETSVGYYNLEVISEQATAYVIKINELKELLSKNLTHFFYVFQTLQKQVSYSLAKFNDFSINGKLGSICGQLLILTYVYGKETPDGIKITLDNLTMQELGYS-----SSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPKLDEWFYLACPATWGKLN  237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     |   - |     191       201       211       221       231      
                                                                                                                                                                                                         177   183
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BEO)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PRFA_LISMO | P22262)
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: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.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PRFA_LISMO | P22262: 1omi 2bgc 5f1r 5lej 5lek 5lrr 5lrs

(-) Related Entries Specified in the PDB File

1omi CRYSTAL STRUCTURE OF PRFA,THE TRANSCRIPTIONAL REGULATOR INLISTERIA MONOCYTOGENES