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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GEF AND P4M DOMAIN OF DRRA/SIDM FROM LEGIONELLA PNEUMOPHILA
 
Authors :  S. Schoebel, W. Blankenfeldt, R. S. Goody, A. Itzen
Date :  26 May 10  (Deposition) - 28 Jul 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Phosphatidylinositol-4-Phosphate, Membrane, Gef, Rab, Lcv, P4M, Rabgef, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Schoebel, W. Blankenfeldt, R. S. Goody, A. Itzen
High-Affinity Binding Of Phosphatidylinositol 4-Phosphate B Legionella Pneumophila Drra.
Embo Rep. V. 11 598 2010
PubMed-ID: 20616805  |  Reference-DOI: 10.1038/EMBOR.2010.97

(-) Compounds

Molecule 1 - GUANINE NUCLEOTIDE EXCHANGE FACTOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET19MOD_TEV
    Expression System StrainBL21(DE3) RIL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentGEF AND P4M DOMAINS (UNP RESIDUES 340-647)
    GeneDRRA, LPG2464
    Organism ScientificLEGIONELLA PNEUMOPHILA
    Organism Taxid272624
    StrainPHILADELPHIA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:22 , HOH A:59 , HOH A:131 , TYR A:532 , ARG A:541 , LYS A:568 , GLN A:608 , THR A:619 , SER A:620 , SER A:621BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWAREHOH B:26 , HOH B:74 , TYR B:532 , ARG B:541 , LYS B:568 , GLN B:608 , THR B:619 , SER B:620 , SER B:621BINDING SITE FOR RESIDUE SO4 B 2
3AC3SOFTWAREHOH A:16 , HOH A:56 , HOH A:139 , HIS A:376 , LYS A:380 , ARG A:544 , GLY A:609 , LEU A:610 , THR A:611BINDING SITE FOR RESIDUE SO4 A 3
4AC4SOFTWAREHOH B:43 , HOH B:63 , HIS B:376 , LYS B:380 , ARG B:544 , GLY B:609 , LEU B:610 , THR B:611BINDING SITE FOR RESIDUE SO4 B 4
5AC5SOFTWAREHOH A:16 , HOH A:56 , HOH A:132 , HIS A:543 , GLN A:608 , GLY A:609 , THR A:612BINDING SITE FOR RESIDUE SO4 A 5
6AC6SOFTWAREHOH B:63 , HOH B:135 , HIS B:543 , GLN B:608 , GLY B:609 , THR B:612BINDING SITE FOR RESIDUE SO4 B 6
7AC7SOFTWAREARG A:390 , HOH B:96 , ARG B:563BINDING SITE FOR RESIDUE SO4 A 7
8AC8SOFTWAREARG A:563 , ARG B:390 , PRO B:391BINDING SITE FOR RESIDUE SO4 B 8

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N6O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3N6O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N6O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N6O)

(-) Exons   (0, 0)

(no "Exon" information available for 3N6O)

(-) 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:303
 aligned with DRRA_LEGPH | Q5ZSQ3 from UniProtKB/Swiss-Prot  Length:647

    Alignment length:303
                                   346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636   
           DRRA_LEGPH   337 VQRVTRIENLENAKKLWDNANSMLEKGNISGYLKAANELHKFMKEKNLKEDDLRPELSDKTISPKGYAILQSLWGAASDYSRAAATLTESTVEPGLVSAVNKMSAFFMDCKLSPNERATPDPDFKVGKSKILVGIMQFIKDVADPTSKIWMHNTKALMNHKIAAIQKLERSNNVNDETLESVLSSKGENLSEYLSYKYATKDEGREHRYTASTENFKNVKEKYQQMRGDALKTEILADFKDKLAEATDEQSLKQIVAELKSKDEYRILAKGQGLTTQLLGLKTSSVSSFEKMVEETRESIKSQ 639
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh....ee..eehhhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhh.........................hhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n6o A 337 GHMVTRIENLENAKKLWDNANSMLEKGNISGYLKAANELHKFMKEKNLKEDDLRPELSDKTISPKGYAILQSLWGAASDYSRAAATLTESTVEPGLVSAVNKMSAFFMDCKLSPNERATPDPDFKVGKSKILVGIMQFIKDVADPTSKIWMHNTKALMNHKIAAIQKLERSNNVNDETLESVLSSKGENLSEYLSYKYATKDEGREHRYTASTENFKNVKEKYQQMRGDALKTEILADFKDKLAEATDEQSLKQIVAELKSKDEYRILAKGQGLTTQLLGLKTSSVSSFEKMVEETRESIKSQ 639
                                   346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636   

Chain B from PDB  Type:PROTEIN  Length:301
 aligned with DRRA_LEGPH | Q5ZSQ3 from UniProtKB/Swiss-Prot  Length:647

    Alignment length:301
                                   346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636 
           DRRA_LEGPH   337 VQRVTRIENLENAKKLWDNANSMLEKGNISGYLKAANELHKFMKEKNLKEDDLRPELSDKTISPKGYAILQSLWGAASDYSRAAATLTESTVEPGLVSAVNKMSAFFMDCKLSPNERATPDPDFKVGKSKILVGIMQFIKDVADPTSKIWMHNTKALMNHKIAAIQKLERSNNVNDETLESVLSSKGENLSEYLSYKYATKDEGREHRYTASTENFKNVKEKYQQMRGDALKTEILADFKDKLAEATDEQSLKQIVAELKSKDEYRILAKGQGLTTQLLGLKTSSVSSFEKMVEETRESIK 637
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh....ee..eehhhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhh.........................hhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n6o B 337 GHMVTRIENLENAKKLWDNANSMLEKGNISGYLKAANELHKFMKEKNLKEDDLRPELSDKTISPKGYAILQSLWGAASDYSRAAATLTESTVEPGLVSAVNKMSAFFMDCKLSPNERATPDPDFKVGKSKILVGIMQFIKDVADPTSKIWMHNTKALMNHKIAAIQKLERSNNVNDETLESVLSSKGENLSEYLSYKYATKDEGREHRYTASTENFKNVKEKYQQMRGDALKTEILADFKDKLAEATDEQSLKQIVAELKSKDEYRILAKGQGLTTQLLGLKTSSVSSFEKMVEETRESIK 637
                                   346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636 

   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 3N6O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N6O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3N6O)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DRRA_LEGPH | Q5ZSQ3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0017137    Rab GTPase binding    Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    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:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0070273    phosphatidylinositol-4-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' position.
    GO:0070733    protein adenylyltransferase activity    Catalysis of the reaction: ATP + protein = diphosphate + adenylyl-protein; mediates the addition of an adenylyl (adenosine 5'-monophosphate; AMP group) to specific residues of target proteins.
    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:0044600    protein guanylyltransferase activity    Catalysis of the reaction: GTP + protein = diphosphate + guanylyl-protein; mediates the addition of an guanylyl (guanosine 5'-monophosphate; GMP group) to specific residues of target proteins.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0018117    protein adenylylation    The addition of an adenylyl group (adenosine 5'-monophosphate; AMP) to a protein amino acid.
    GO:0018260    protein guanylylation    The addition of phospho-guanosine to a protein amino acid.
    GO:0006612    protein targeting to membrane    The process of directing proteins towards a membrane, usually using signals contained within the protein.
    GO:0043087    regulation of GTPase activity    Any process that modulates the rate of GTP hydrolysis by a GTPase.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0044161    host cell cytoplasmic vesicle    A vesicle formed of membrane or protein, found in the cytoplasm of a host cell.
    GO:0044162    host cell cytoplasmic vesicle membrane    The lipid bilayer surrounding a host cell cytoplasmic vesicle.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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.
    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/Swiss-Prot
        DRRA_LEGPH | Q5ZSQ32wwx 3jz9 3jza 3l0i 3l0m 4mxp

(-) Related Entries Specified in the PDB File

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