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(-) Description

Title :  CANINE GDP-RAN
 
Authors :  M. Stewart, H. M. Kent, A. J. Mccoy
Date :  18 Oct 98  (Deposition) - 02 Dec 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gtpase, Nuclear Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Stewart, H. M. Kent, A. J. Mccoy
The Structure Of The Q69L Mutant Of Gdp-Ran Shows A Major Conformational Change In The Switch Ii Loop That Accounts For Its Failure To Bind Nuclear Transport Factor 2 (Ntf2).
J. Mol. Biol. V. 284 1517 1998
PubMed-ID: 9878368  |  Reference-DOI: 10.1006/JMBI.1998.2204
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (GTP-BINDING PROTEIN RAN)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Fragment: ALL
    Organism Common: DOG
    Organism Scientific: CANIS LUPUS FAMILIARIS
    Organism Taxid: 9615
    Strain: BL21(DE3)
    Synonym: TC4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:24 , GDP A:220 , HOH A:246 , HOH A:247 , HOH A:248 , HOH A:249BINDING SITE FOR RESIDUE MG A 221
2AC2SOFTWARETHR B:24 , GDP B:220 , HOH B:246 , HOH B:247 , HOH B:248 , HOH B:249BINDING SITE FOR RESIDUE MG B 221
3AC3SOFTWAREGLY A:20 , THR A:21 , GLY A:22 , LYS A:23 , THR A:24 , THR A:25 , ASN A:122 , LYS A:123 , ASP A:125 , ALA A:151 , LYS A:152 , MG A:221 , HOH A:246 , HOH A:247 , HOH A:249 , HOH A:275BINDING SITE FOR RESIDUE GDP A 220
4AC4SOFTWAREHOH A:317 , GLY B:20 , THR B:21 , GLY B:22 , LYS B:23 , THR B:24 , THR B:25 , ASN B:122 , LYS B:123 , ASP B:125 , ALA B:151 , LYS B:152 , MG B:221 , HOH B:246 , HOH B:247 , HOH B:249 , HOH B:283BINDING SITE FOR RESIDUE GDP B 220

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BYU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BYU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BYU)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RANPS51418 small GTPase Ran family profile.RAN_CANLF4-168  1B:4-168

(-) Exons   (0, 0)

(no "Exon" information available for 1BYU)

(-) 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:202
 aligned with RAN_CANLF | P62825 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:202
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205  
            RAN_CANLF     6 EPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTT 207
               SCOP domains d1byua_ A: Ran                                                                                                                                                                                             SCOP domains
               CATH domains 1byuA00 A:6-207 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee.....hhhhhhh.hhhhh..eee....eeeeeeeeee..eeeeeeeeee..hhh.....hhhh....eeeeeee...hhhhh.hhhhhhhhhhhh...eeeeeee..........hhhhhhhhhh..eeee..hhh.....hhhhhhhhhhh.....................hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RAN  PDB: - UniProt: 4-168                                                                                                                                         --------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1byu A   6 EPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVPTLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTT 207
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205  


Chain B from PDB  Type:PROTEIN  Length:215
 aligned with RAN_CANLF | P62825 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
            RAN_CANLF     2 AAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL 216
               SCOP domains d1byub_ B: Ran                                                                                                                                                                                                          SCOP domains
               CATH domains 1byuB00 B:2-216 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee......hhhhhhh.hhhhh..eee....eeeeeeeeee..eeeeeeeeee..hhh.....hhhh....eeeeeee...hhhhh.hhhhhhhhhhhh...eeeeeee..........hhhhhh.....eeeeee.hhh.....hhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RAN  PDB: B:4-168 UniProt: 4-168                                                                                                                                     ------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1byu B   2 AAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVPTLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL 216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BYU)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RAN_CANLF | P62825)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    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.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:0006913    nucleocytoplasmic transport    The directed movement of molecules between the nucleus and the cytoplasm.
    GO:0006606    protein import into nucleus    The directed movement of a protein from the cytoplasm to the nucleus.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0000054    ribosomal subunit export from nucleus    The directed movement of a ribosomal subunit from the nucleus into the cytoplasm.
    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.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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        RAN_CANLF | P62825: 1a2k 1qg2 1qg4 1wa5 2bku 3a6p 3ran 3w3z 5bxq

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