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(-) Description

Title :  CRYSTAL STRUCTURE OF GYP1 TBC DOMAIN IN COMPLEX WITH RAB33 GTPASE BOUND TO GDP AND ALF3
 
Authors :  X. Pan, S. Eathiraj, M. Munson, D. G. Lambright
Date :  27 Feb 06  (Deposition) - 25 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Transport, Gyp1 Tbc Domain, Rab33, Vesicular Trafficking, Hydrolase Activator/Protein Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Pan, S. Eathiraj, M. Munson, D. G. Lambright
Tbc-Domain Gaps For Rab Gtpases Accelerate Gtp Hydrolysis By A Dual-Finger Mechanism.
Nature V. 442 303 2006
PubMed-ID: 16855591  |  Reference-DOI: 10.1038/NATURE04847
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GTPASE-ACTIVATING PROTEIN GYP1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidMODIFIED PET15B
    Expression System StrainBL21(DE3) RIL CODON PLUS
    Expression System Taxid562
    Expression System Vector TypePET15B
    FragmentGYP1 TBC DOMAIN
    GeneGYP1
    MutationYES
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymGAP FOR YPT1
 
Molecule 2 - RAS-RELATED PROTEIN RAB-33B
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidMODIFIED PET15B
    Expression System StrainBL21(DE3) RIL CODON PLUS
    Expression System Taxid562
    Expression System Vector TypePET15B
    GeneRAB33B
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1AF31Ligand/IonALUMINUM FLUORIDE
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION
4MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:47 , THR B:65 , GDP B:501 , AF3 B:502 , HOH B:504 , HOH B:632BINDING SITE FOR RESIDUE MG B 503
2AC2SOFTWAREARG A:343 , ASN B:43 , VAL B:44 , GLY B:45 , LYS B:46 , THR B:47 , CYS B:48 , PHE B:58 , THR B:62 , ASN B:148 , LYS B:149 , ASP B:151 , SER B:178 , ALA B:179 , LYS B:180 , AF3 B:502 , MG B:503 , HOH B:534 , HOH B:537 , HOH B:551 , HOH B:564 , HOH B:568 , HOH B:601 , HOH B:632BINDING SITE FOR RESIDUE GDP B 501
3AC3SOFTWAREARG A:343 , GLN A:378 , SER B:42 , ASN B:43 , LYS B:46 , ALA B:64 , THR B:65 , THR B:89 , ALA B:90 , GLY B:91 , GDP B:501 , MG B:503 , HOH B:550BINDING SITE FOR RESIDUE AF3 B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2G77)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2G77)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G77)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TBC_RABGAPPS50086 TBC/rab GAP domain profile.GYP1_YEAST280-508  1A:280-508

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YOR070C1YOR070C.1XV:457822-4559091914GYP1_YEAST1-6376371A:246-633 (gaps)388

(-) 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:331
 aligned with GYP1_YEAST | Q08484 from UniProtKB/Swiss-Prot  Length:637

    Alignment length:388
                                   255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625        
           GYP1_YEAST   246 QELNSIIQRISKFDNILKDKTIINQQDLRQISWNGIPKIHRPVVWKLLIGYLPVNTKRQEGFLQRKRKEYRDSLKHTFSDQHSRDIPTWHQIEIDIPRTNPHIPLYQFKSVQNSLQRILYLWAIRHPASGYVQGINDLVTPFFETFLTEYLPPSQIDDVEIKDPSTYMVDEQITDLEADTFWCLTKLLEQITDNYIHGQPGILRQVKNLSQLVKRIDADLYNHFQNEHVEFIQFAFRWMNCLLMREFQMGTVIRMWDTYLSETSQEVTSSYSMSSNDIKPPVTPTEPRVASFVTPTKDFQSPTTALSNMTPNNAVEDSGKMRQSSLNEFHVFVCAAFLIKWSDQLMEMDFQETITFLQNPPTKDWTETDIEMLLSEAFIWQSLYKDAT 633
               SCOP domains d2g77a1 A:246-442 Ypt/Rab-GAP domain of gyp1p                                                                                                                                                        d2g77a2 A:443-633 Ypt/Rab-GAP domain of gyp1p                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.....hhhhhhhhhh......hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..---------------------------------------------------------..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------TBC_RABGAP  PDB: A:280-508 UniProt: 280-508                                                                                                                                                                                          ----------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:246-633 (gaps) UniProt: 1-637 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                          Transcript 1
                 2g77 A 246 QELNSIIQRISKFDNILKDKTIINQQDLRQISWNGIPKIHRPVVWKLLIGYLPVNTKRQEGFLQRKRKEYRDSLKHTFSDQHSRDIPTWHQIEIDIPRTNPHIPLYQFKSVQNSLQRILYLWAIRHPASGYVQGINDLVTPFFETFLTEYLPPSQIDDVKIKDPSTYMVDEQITDLEADTFWCLTKLLEQITDNYIHGQPGILRQVKNLSQLVKRIDADLYNHFQNEHVEFIQFAFRWMNCLLMREFQMGTVIRMWDTYLSETSQ---------------------------------------------------------QSSLNEFHVFVCAAFLIKWSDQLMEMDFQETITFLQNPPTKDWTETDIEMLLSEAFIWQSLYKDAT 633
                                   255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505    |    -         -         -         -         -         -  |    575       585       595       605       615       625        
                                                                                                                                                                                                                                                                                                  510                                                       568                                                                 

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with RB33B_MOUSE | O35963 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:173
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199   
          RB33B_MOUSE    30 RSRIFKIIVIGDSNVGKTCLTYRFCAGRFPDRTEATIGVDFRERAVDIDGERIKIQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDMTNMASFHSLPAWIEECKQHLLANDIPRILVGNKCDLRSAIQVPTDLAQKFADTHSMPLFETSAKNPNDNDHVEAIFMTLAHKLKSH 202
               SCOP domains d2g77b1 B:30-202 Rab-33b                                                                                                                                                      SCOP domains
               CATH domains 2g77B00 B:30-202 P-loop containing nucleotide triphosphate hydrolases                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhhh.hhhhhh....eeeeeee..hhhhhhhhhhhhhhhhh........eeeeee...hhhhh..hhhhhhhhhhhh...eee....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g77 B  30 RSRIFKIIVIGDSNVGKTCLTYRFCAGRFPDRTEATIGVDFRERAVDIDGERIKIQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDmTNmASFHSLPAWIEECKQHLLANDIPRILVGNKCDLRSAIQVPTDLAQKFADTHSmPLFETSAKNPNDNDHVEAIFmTLAHKLKSH 202
                                    39        49        59        69        79        89        99       109      |119       129       139       149       159       169  |    179       189   |   199   
                                                                                                                116-MSE                                                 172-MSE              193-MSE     
                                                                                                                   119-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  (2, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G77)

(-) Gene Ontology  (27, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GYP1_YEAST | Q08484)
molecular function
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    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.
biological process
    GO:0090630    activation of GTPase activity    Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
    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:0031338    regulation of vesicle fusion    Any process that modulates the frequency, rate or extent of vesicle fusion.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
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:0005795    Golgi stack    The set of thin, flattened membrane-bounded compartments, called cisternae, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack.

Chain B   (RB33B_MOUSE | O35963)
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.
    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:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0006891    intra-Golgi vesicle-mediated transport    The directed movement of substances within the Golgi, mediated by small transport vesicles. These either fuse with the cis-Golgi or with each other to form the membrane stacks known as the cis-Golgi reticulum (network).
    GO:1903434    negative regulation of constitutive secretory pathway    Any process that stops, prevents or reduces the frequency, rate or extent of constitutive secretory pathway.
    GO:0000042    protein targeting to Golgi    The process of directing proteins towards the Golgi; usually uses signals contained within the protein.
    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:1903358    regulation of Golgi organization    Any process that modulates the frequency, rate or extent of Golgi organization.
    GO:2000785    regulation of autophagosome assembly    Any process that modulates the frequency, rate or extent of autophagosome assembly.
    GO:2000156    regulation of retrograde vesicle-mediated transport, Golgi to ER    Any process that modulates the frequency, rate or extent of retrograde vesicle-mediated transport, Golgi to ER.
    GO:0048705    skeletal system morphogenesis    The process in which the anatomical structures of the skeleton are generated and organized.
    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: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:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    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: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
        GYP1_YEAST | Q084841fkm
        RB33B_MOUSE | O359631z06

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2G77)