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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PLANT RHO PROTEIN ROP5
 
Authors :  C. Thomas, A. Berken
Date :  09 Jan 08  (Deposition) - 11 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym./Biol. Unit :  D
Keywords :  G Domain, Cytoplasm, Gtp-Binding, Lipoprotein, Membrane, Methylation, Nucleotide-Binding, Prenylation, ----, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Thomas, A. Berken
Crystal Structure Of The Plant Rho Protein Rop5
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAC-LIKE GTP-BINDING PROTEIN ARAC6
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T-1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-180
    Gene: ARAC6, RAC2, ROP5
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: GTPASE PROTEIN ROP5, PLANT RHO PROTEIN ROP5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR D:20 , HOH D:209 , HOH D:210 , HOH D:224 , HOH D:225BINDING SITE FOR RESIDUE MG D 181
2AC2SOFTWAREALA D:16 , GLY D:18 , LYS D:19 , THR D:20 , CYS D:21 , PHE D:31 , LYS D:119 , ASP D:121 , LEU D:122 , SER D:159 , SER D:160 , LYS D:161 , HOH D:208 , HOH D:210 , HOH D:224 , HOH D:235BINDING SITE FOR RESIDUE GDP D 200

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BWD)

(-) 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 D from PDB  Type:PROTEIN  Length:156
 aligned with RAC6_ARATH | Q9SBJ6 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174      
           RAC6_ARATH     5 RFIKCVTVGDGAVGKTCLLISYTSNTFPTDYVPTVFDNFSANVVVNGATVNLGLWDTAGQEDYNRLRPLSYRGADVFILAFSLISKASYENVSKKWIPELKHYAPGVPIVLVGTKLDLRDDKQFFIDHPGAVPITTVQGEELKKLIGAPAYIECSSKSQENVKGVFDAAIRVVLQP 180
               SCOP domains d3bwdd_ D: automated matches                                                                                                                                                     SCOP domains
               CATH domains 3bwdD00 D:5-180 P-loop conta          ining        nucleoti de triphosphate hydrolases                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhh...----------......-------.eee....-.....hhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh--....hhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bwd D   5 RFIKCVTVGDGAVGKTCLLISYTSNTFP----------FSANVV-------LGLWDTAG-EDYNRLRPLSYRGADVFILAFSLISKASYENVSKKWIPELKHYAPGVPIVLVGTKLDLRDDKQFFIDH--AVPITTVQGEELKKLIGAPAYIECSSKSQENVKGVFDAAIRVVLQP 180
                                    14        24       | -        44   |     - |      |-|       74        84        94       104       114       124       | -|      144       154       164       174      
                                                      32         43   48      56     63 |                                                                132  |                                             
                                                                                       65                                                                   135
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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  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain D   (RAC6_ARATH | Q9SBJ6)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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).
biological process
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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