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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GEF DOMAIN OF DRRA/SIDM FROM LEGIONELLA PNEUMOPHILA
 
Authors :  S. Schoebel, L. K. Oesterlin, W. Blankenfeldt, R. S. Goody, A. Itzen
Date :  23 Sep 09  (Deposition) - 19 Jan 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Rabgdi, Rabgef, Gdi, Gef, Gdf, Gdi Displacement Factor, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Schoebel, L. K. Oesterlin, W. Blankenfeldt, R. S. Goody, A. Itzen
Rabgdi Displacement By Drra From Legionella Is A Consequenc Of Its Guanine Nucleotide Exchange Activity.
Mol. Cell V. 36 1060 2009
PubMed-ID: 20064470  |  Reference-DOI: 10.1016/J.MOLCEL.2009.11.014
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN DRRA
    Atcc33152
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET19MOD_TEV
    Expression System StrainBL21(DE3)RIL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneLPG2464
    Organism ScientificLEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA STR. PHILADELPHIA 1
    Organism Taxid272624
    StrainPHILADELPHIA 1 / DSM 7513

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3JZ9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JZ9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3JZ9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JZ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JZ9)

(-) Exons   (0, 0)

(no "Exon" information available for 3JZ9)

(-) 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:197
 aligned with DRRA_LEGPH | Q5ZSQ3 from UniProtKB/Swiss-Prot  Length:647

    Alignment length:197
                                   346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       
           DRRA_LEGPH   337 VQRVTRIENLENAKKLWDNANSMLEKGNISGYLKAANELHKFMKEKNLKEDDLRPELSDKTISPKGYAILQSLWGAASDYSRAAATLTESTVEPGLVSAVNKMSAFFMDCKLSPNERATPDPDFKVGKSKILVGIMQFIKDVADPTSKIWMHNTKALMNHKIAAIQKLERSNNVNDETLESVLSSKGENLSEYLSYK 533
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh....ee..eehhhhhhhhhhhhhhhhhh...hhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jz9 A 337 GHmVTRIENLENAKKLWDNANSmLEKGNISGYLKAANELHKFmKEKNLKEDDLRPELSDKTISPKGYAILQSLWGAASDYSRAAATLTESTVEPGLVSAVNKmSAFFmDCKLSPNERATPDPDFKVGKSKILVGImQFIKDVADPTSKIWmHNTKALmNHKIAAIQKLERSNNVNDETLESVLSSKGENLSEYLSYK 533
                              |    346       356  |    366       376  |    386       396       406       416       426       436  |    446       456       466     | 476       486|      496       506       516       526       
                              |                 359-MSE             379-MSE                                                     439-MSE|                         472-MSE        487-MSE  |                                       
                            339-MSE                                                                                                  444-MSE                                           494-MSE                                   

   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 3JZ9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JZ9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3JZ9)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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 3jza 3l0i 3l0m 3n6o 4mxp

(-) Related Entries Specified in the PDB File

3jza CRYSTAL STRUCTURE OF HUMAN RAB1B IN COMPLEX WITH THE GEF DOMAIN OF DRRA/SIDM FROM LEGIONELLA PNEUMOPHILA