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(-) Description

Title :  STRUCTURE OF SMALL GTPASE HUMAN RHEB IN COMPLEX WITH GDP
 
Authors :  Y. Yu, J. Ding
Date :  24 Oct 04  (Deposition) - 08 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Saddle, P-Loop, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Yu, S. Li, X. Xu, Y. Li, K. Guan, E. Arnold, J. Ding
Structural Basis For The Unique Biological Function Of Small Gtpase Rheb
J. Biol. Chem. V. 280 17093 2005
PubMed-ID: 15728574  |  Reference-DOI: 10.1074/JBC.M501253200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GTP-BINDING PROTEIN RHEB
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET22B(+)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentGTPASE DOMAIN
    GeneRHEB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRAS HOMOLOG ENRICHED IN BRAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

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
1AC1SOFTWARESER A:20 , GDP A:201 , HOH A:203 , HOH A:204 , HOH A:205 , HOH A:206BINDING SITE FOR RESIDUE MG A 202
2AC2SOFTWARESER A:16 , VAL A:17 , GLY A:18 , LYS A:19 , SER A:20 , SER A:21 , PHE A:31 , ASN A:119 , LYS A:120 , ASP A:122 , LEU A:123 , SER A:149 , ALA A:150 , LYS A:151 , MG A:202 , HOH A:203 , HOH A:204 , HOH A:208 , HOH A:268 , HOH A:325 , HOH A:331 , HOH A:343 , HOH A:355BINDING SITE FOR RESIDUE GDP A 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036310E139KRHEB_HUMANUnclassified  ---AE139K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XTQ)

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002621871bENSE00001200523chr7:151217010-151216546465RHEB_HUMAN1-18181A:3-1816
1.5ENST000002621875ENSE00000730260chr7:151188100-15118802972RHEB_HUMAN18-42251A:18-4225
1.6ENST000002621876ENSE00000909920chr7:151181890-15118182368RHEB_HUMAN42-64231A:42-6423
1.7ENST000002621877ENSE00000730253chr7:151174501-15117441983RHEB_HUMAN65-92281A:65-9228
1.8cENST000002621878cENSE00001139595chr7:151168691-15116863557RHEB_HUMAN92-111201A:92-11120
1.8fENST000002621878fENSE00001200505chr7:151168527-15116848048RHEB_HUMAN111-127171A:111-12717
1.9aENST000002621879aENSE00001315618chr7:151167738-15116765782RHEB_HUMAN127-154281A:127-15428
1.10dENST0000026218710dENSE00001321653chr7:151164297-1511630981200RHEB_HUMAN155-184301A:155-17117

(-) 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:169
 aligned with RHEB_HUMAN | Q15382 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:169
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162         
           RHEB_HUMAN     3 QSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVDTAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAESWNAAFLESSAKENQTAVDVFRRIILEAEKMD 171
               SCOP domains d1xtqa1 A:3-169 GTP-binding protein RheB                                                                                                                               -- SCOP domains
               CATH domains 1xtqA00 A:3-171 P-loop containing nucleotide triphosphate hydrolases                                                                                                      CATH domains
               Pfam domains -----Ras-1xtqA01 A:8-169                                                                                                                                               -- Pfam domains
         Sec.struct. author ..eeeeeeeee....hhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee..........hhhhh....eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhh..hhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------K-------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b       -----------------------Exon 1.6  PDB: A:42-64 Exon 1.7  PDB: A:65-92      ------------------Exon 1.8f        ---------------------------Exon 1.10d        Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.5  PDB: A:18-42   -------------------------------------------------Exon 1.8c           ---------------Exon 1.9a  PDB: A:127-154   ----------------- Transcript 1 (2)
                 1xtq A   3 QSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVDTAGQDEYSIFPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAESWNAAFLESSAKENQTAVDVFRRIILEAEKLE 171
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162         

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Family: Ras (176)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RHEB_HUMAN | Q15382)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0016236    macroautophagy    The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
    GO:0032008    positive regulation of TOR signaling    Any process that activates or increases the frequency, rate or extent of TOR signaling.
    GO:0048714    positive regulation of oligodendrocyte differentiation    Any process that activates or increases the frequency, rate or extent of oligodendrocyte differentiation.
    GO:0032006    regulation of TOR signaling    Any process that modulates the frequency, rate or extent of TOR signaling.
    GO:2000074    regulation of type B pancreatic cell development    Any process that modulates the frequency, rate or extent of pancreatic B cell development.
    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.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005681    spliceosomal complex    Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RHEB_HUMAN | Q153821xtr 1xts 3sea 3t5g

(-) Related Entries Specified in the PDB File

1xtr THE SAME PROTEIN IN COMPLEX WITH GPPNHP
1xts THE SAME PROTEIN IN COMPLEX WITH GTP