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(-) Description

Title :  CRYSTAL STRUCTURE OF VIRULENCE FACTOR REGULATOR FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH CAMP
 
Authors :  T. J. Cordes, A. R. Bright, K. T. Forest
Date :  24 Feb 07  (Deposition) - 04 Mar 08  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Winged Helix, Helix-Turn-Helix, Transcription Factor, Camp-Binding Proteins, Camp Receptor Protein, Nucleotide Binding Proteins, Dna- Binding Proteins, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. J. Cordes, G. A. Worzalla, A. M. Ginster, K. T. Forest
Crystal Structure Of The Pseudomonas Aeruginosa Virulence Factor Regulator.
J. Bacteriol. V. 193 4069 2011
PubMed-ID: 21665969  |  Reference-DOI: 10.1128/JB.00666-10

(-) Compounds

Molecule 1 - VIRULENCE FACTOR REGULATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3) DELTA CRP
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: VFR
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Strain: PAK

 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, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CMP2Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CMP4Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:59 , GLU A:60 , ALA A:140 , GLN A:175 , GLY A:178 , ARG A:179 , GLY A:182 , CYS A:183 , SER A:184 , ARG A:185BINDING SITE FOR RESIDUE CMP A 302
2AC2SOFTWARECYS A:38 , ILE A:63 , PHE A:72 , GLY A:73 , GLU A:74 , LEU A:75 , GLY A:76 , ARG A:87 , SER A:88 , ALA A:89 , ARG A:128 , LEU A:129 , THR A:132 , THR A:133 , HOH A:311BINDING SITE FOR RESIDUE CMP A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OZ6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OZ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OZ6)

(-) PROSITE Motifs  (4, 4)

Asymmetric Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_1PS00888 Cyclic nucleotide-binding domain signature 1.VFR_PSEAE31-47  1A:31-47
2CNMP_BINDING_2PS00889 Cyclic nucleotide-binding domain signature 2.VFR_PSEAE72-93  1A:72-93
3HTH_CRP_2PS51063 Crp-type HTH domain profile.VFR_PSEAE142-214  1A:142-213
4HTH_CRP_1PS00042 Crp-type HTH domain signature.VFR_PSEAE172-195  1A:172-195
Biological Unit 1 (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_1PS00888 Cyclic nucleotide-binding domain signature 1.VFR_PSEAE31-47  2A:31-47
2CNMP_BINDING_2PS00889 Cyclic nucleotide-binding domain signature 2.VFR_PSEAE72-93  2A:72-93
3HTH_CRP_2PS51063 Crp-type HTH domain profile.VFR_PSEAE142-214  2A:142-213
4HTH_CRP_1PS00042 Crp-type HTH domain signature.VFR_PSEAE172-195  2A:172-195

(-) Exons   (0, 0)

(no "Exon" information available for 2OZ6)

(-) 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:201
 aligned with VFR_PSEAE | P55222 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:206
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207      
            VFR_PSEAE     8 PKLKHLDKLLAHCHRRRYTAKSTIIYAGDRCETLFFIIKGSVTILIEDDDGREMIIGYLNSGDFFGELGLFEKEGSEQERSAWVRAKVECEVAEISYAKFRELSQQDSEILYTLGSQMADRLRKTTRKVGDLAFLDVTGRVARTLLDLCQQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKSLEEQGLVHVKGKTMVVFGT 213
               SCOP domains -d2oz6a2 A:9-142 Cyclic AMP receptor-like protein Vfr                                                                                  d2oz6a1 A:143-213 Cyclic AMP receptor-like protein Vfr                  SCOP domains
               CATH domains ---2oz6A01 A:11-142 Jelly Rolls                                                                                                        2oz6A02 A:143-211 'winged helix' repressor DNA binding domain        -- CATH domains
               Pfam domains --------------cNMP_binding-2oz6A02 A:22-116                                                                  -----------------------------------------------------Crp-2oz6A01 A:170-201           ------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh.eeeee....eee.......eeeeeee.eeeeeee.....eeeeeeee...ee.......-----.....eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee..eeeee.hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------CNMP_BINDING_1   ------------------------CNMP_BINDING_2        ------------------------------------------------HTH_CRP_2  PDB: A:142-213 UniProt: 142-214                               PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------HTH_CRP_1  PDB: A:172-19------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oz6 A   8 MKLKHLDKLLAHCHRRRYTAKSTIIYAGDRCETLFFIIKGSVTILIEDDDGREMIIGYLNSGDFFGELGLFE-----QERSAWVRAKVECEVAEISYAKFRELSQQDSEILYTLGSQMADRLRKTTRKVGDLAFLDVTGRVARTLLDLCQQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKSLEEQGLVHVKGKTMVVFGT 213
                                    17        27        37        47        57        67        77 |     |87        97       107       117       127       137       147       157       167       177       187       197       207      
                                                                                                  79    85
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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: All beta proteins (24004)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Clan: no clan defined [family: cNMP_binding] (41)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (VFR_PSEAE | P55222)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0030552    cAMP binding    Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0043902    positive regulation of multi-organism process    Any process that activates or increases the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species.
    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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