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(-) Description

Title :  STRUCTURE OF PSEUDOMONAS FLUORESCENCE LAPD EAL DOMAIN COMPLEXED WITH C-DI-GMP, C2221
 
Authors :  H. Sondermann, M. V. A. S. Navarro, P. Krasteva
Date :  10 Nov 10  (Deposition) - 09 Feb 11  (Release) - 23 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.52
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrel, C-Di-Gmp Receptor, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. V. Navarro, P. D. Newell, P. V. Krasteva, D. Chatterjee, D. R. Madden G. A. O'Toole, H. Sondermann
Structural Basis For C-Di-Gmp-Mediated Inside-Out Signaling Controlling Periplasmic Proteolysis.
Plos Biol. V. 9 E1000 2011
PubMed-ID: 21304926  |  Reference-DOI: 10.1371/JOURNAL.PBIO.1000588

(-) Compounds

Molecule 1 - CYCLIC DIMERIC GMP BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 400-648
    Gene: LAPD, PFL01_0131
    Organism Scientific: PSEUDOMONAS FLUORESCENS
    Organism Taxid: 205922
    Strain: PF0-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1C2E2Ligand/Ion9,9'-[(2R,3R,3AS,5S,7AR,9R,10R,10AS,12S,14AR)-3,5,10,12-TETRAHYDROXY-5,12-DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-2,9-DIYL]BIS(2-AMINO-1,9-DIHYDRO-6H-PURIN-6-ONE)

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2 , HOH A:18 , HOH A:27 , HOH A:40 , HOH A:50 , GLN A:431 , LYS A:446 , LEU A:448 , SER A:449 , ARG A:450 , PRO A:460 , ALA A:461 , GLY A:462 , LEU A:465 , ASP A:478 , MET A:481 , ASN A:499 , GLN A:560 , ARG A:561 , ARG A:618 , VAL A:619 , GLU A:620 , GLY A:638 , GLN A:639 , PRO A:644BINDING SITE FOR RESIDUE C2E A 2256
2AC2SOFTWAREHOH B:17 , HOH B:84 , GLN B:431 , LYS B:446 , LEU B:448 , SER B:449 , ARG B:450 , PRO B:460 , ALA B:461 , GLY B:462 , LEU B:465 , ASP B:478 , MET B:481 , ASN B:499 , GLN B:560 , ARG B:561 , ARG B:618 , VAL B:619 , GLU B:620 , GLY B:638 , GLN B:639 , PRO B:644BINDING SITE FOR RESIDUE C2E B 2256

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe B:562 -Gly B:563

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PJT)

(-) Exons   (0, 0)

(no "Exon" information available for 3PJT)

(-) 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:240
 aligned with Q3KK31_PSEPF | Q3KK31 from UniProtKB/TrEMBL  Length:648

    Alignment length:240
                                   418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648
         Q3KK31_PSEPF   409 DHHAWHRLLDQALNQRRFELFFQPVVAAQDTQLVLHYKVLSRLLDEQGQTIPAGRFLPWLERFGWTARLDRLMLERVLEQMAGHEESLALNLSSATLADPQALNKVFEILRAHSNLGARLTLEIGEEQLPEQAVLEQLTRRLRELGFSLSLQRFGGRFSMIGNLARLGLAYLKIDGSYIRAIDQESDKRLFIEAIQRAAHSIDLPLIAERVETEGELSVIREMGLYGVQGQLFGEPKPWG 648
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..eeeeeeeeee..eeeeeeeeeeeeeee.....eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhh.hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh...eee.hhhh.....hhhhhhhhhhhhhhhhhh...eee....hhhhhhhhhhh...ee.hhhhh..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pjt A 409 DHHAWHRLLDQALNQRRFELFFQPVVAAQDTQLVLHYKVLSRLLDEQGQTIPAGRFLPWLERFGWTARLDRLMLERVLEQMAGHEESLALNLSSATLADPQALNKVFEILRAHSNLGARLTLEIGEEQLPEQAVLEQLTRRLRELGFSLSLQRFGGRFSMIGNLARLGLAYLKIDGSYIRAIDQESDKRLFIEAIQRAAHSIDLPLIAERVETEGELSVIREMGLYGVQGQLFGEPKPWG 648
                                   418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648


Chain B from PDB  Type:PROTEIN  Length:240
 aligned with Q3KK31_PSEPF | Q3KK31 from UniProtKB/TrEMBL  Length:648

    Alignment length:240
                                   418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648
         Q3KK31_PSEPF   409 DHHAWHRLLDQALNQRRFELFFQPVVAAQDTQLVLHYKVLSRLLDEQGQTIPAGRFLPWLERFGWTARLDRLMLERVLEQMAGHEESLALNLSSATLADPQALNKVFEILRAHSNLGARLTLEIGEEQLPEQAVLEQLTRRLRELGFSLSLQRFGGRFSMIGNLARLGLAYLKIDGSYIRAIDQESDKRLFIEAIQRAAHSIDLPLIAERVETEGELSVIREMGLYGVQGQLFGEPKPWG 648
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----EAL-3pjtB01 B:414-644                                                                                                                                                                                                                  ---- Pfam domains (1)
           Pfam domains (2) -----EAL-3pjtB02 B:414-644                                                                                                                                                                                                                  ---- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhh..eeeeeeeeee......eeeeeeeeeee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhh.hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh...eee.hhhh.hhhhhhhhhhhhhhhhhhhhhh...eee....hhhhhhhhhhh...ee.hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pjt B 409 DHHAWHRLLDQALNQRRFELFFQPVVAAQDTQLVLHYKVLSRLLDEQGQTIPAGRFLPWLERFGWTARLDRLMLERVLEQMAGHEESLALNLSSATLADPQALNKVFEILRAHSNLGARLTLEIGEEQLPEQAVLEQLTRRLRELGFSLSLQRFGGRFSMIGNLARLGLAYLKIDGSYIRAIDQESDKRLFIEAIQRAAHSIDLPLIAERVETEGELSVIREMGLYGVQGQLFGEPKPWG 648
                                   418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648
   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 3PJT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: EAL] (10)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q3KK31_PSEPF | Q3KK31)
molecular function
    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: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:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/TrEMBL
        Q3KK31_PSEPF | Q3KK31: 3pju 3pjv 3pjw 3pjx

(-) Related Entries Specified in the PDB File

3pju 3pjv 3pjw 3pjx