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(-) Description

Title :  CRYSTAL STRUCTURE OF THE YPT/RAB-GAP DOMAIN OF GYP1P
 
Authors :  A. Rak, R. Fedorov, K. Alexandrov, S. Albert, R. S. Goody, D. Gallwitz, A. J. Scheidig
Date :  09 Aug 00  (Deposition) - 09 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Gap, Ypt/Rab Protein, Vesicular Trafficking, Endocytosis, Hydrolase, Gtpase Activation, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Rak, R. Fedorov, K. Alexandrov, S. Albert, R. S. Goody, D. Gallwitz, A. J. Scheidig
Crystal Structure Of The Gap Domain Of Gyp1P: First Insights Into Interaction With Ypt/Rab Proteins.
Embo J. V. 19 5105 2000
PubMed-ID: 11013213  |  Reference-DOI: 10.1093/EMBOJ/19.19.5105
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (GYP1P)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET19
    Expression System StrainBL21/DE3
    Expression System Taxid469008
    FragmentYPT/RAB-GAP DOMAIN, RESIDUES 248-637
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    Other DetailsGENOMIC DNA
    SynonymORF YOR070C

 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 1FKM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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:249-630 (gaps)382

(-) 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:322
 aligned with GYP1_YEAST | Q08484 from UniProtKB/Swiss-Prot  Length:637

    Alignment length:382
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628  
           GYP1_YEAST   249 NSIIQRISKFDNILKDKTIINQQDLRQISWNGIPKIHRPVVWKLLIGYLPVNTKRQEGFLQRKRKEYRDSLKHTFSDQHSRDIPTWHQIEIDIPRTNPHIPLYQFKSVQNSLQRILYLWAIRHPASGYVQGINDLVTPFFETFLTEYLPPSQIDDVEIKDPSTYMVDEQITDLEADTFWCLTKLLEQITDNYIHGQPGILRQVKNLSQLVKRIDADLYNHFQNEHVEFIQFAFRWMNCLLMREFQMGTVIRMWDTYLSETSQEVTSSYSMSSNDIKPPVTPTEPRVASFVTPTKDFQSPTTALSNMTPNNAVEDSGKMRQSSLNEFHVFVCAAFLIKWSDQLMEMDFQETITFLQNPPTKDWTETDIEMLLSEAFIWQSLYK 630
               SCOP domains d1fkma1 A:249-442 Ypt/Rab-GAP domain of gyp1p                                                                                                                                                     d1fkma2 A:443-630 Ypt/Rab-GAP domain of gyp1p                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.....hhhhhhhhhh...hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh------------------------------------------------------------hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh 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:249-630 (gaps) UniProt: 1-637 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                    Transcript 1
                 1fkm A 249 NSIIQRISKFDNILKDKTIINQQDLRQISWNGIPKIHRPVVWKLLIGYLPVNTKRQEGFLQRKRKEYRDSLKHTFSDQHSRDIPTWHQIEIDIPRTNPHIPLYQFKSVQNSLQRILYLWAIRHPASGYVQGINDLVTPFFETFLTEYLPPSQIDDVEIKDPSTYmVDEQITDLEADTFWCLTKLLEQITDNYIHGQPGILRQVKNLSQLVKRIDADLYNHFQNEHVEFIQFAFRWmNCLLmREFQmGTVIRmWDTYLSETS------------------------------------------------------------SLNEFHVFVCAAFLIKWSDQLmEmDFQETITFLQNPPTKDWTETDIEmLLSEAFIWQSLYK 630
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408    |  418       428       438       448       458       468       478     | 488|    | 498 |     508|        -         -         -         -         -         - |     578       588  | |  598       608       618       628  
                                                                                                                                                                                              413-MSE                                                                484-MSE|    |     |      509                                                          570                  591-MSE                   617-MSE         
                                                                                                                                                                                                                                                                          489-MSE|     |                                                                                          593-MSE                                 
                                                                                                                                                                                                                                                                               494-MSE |                                                                                                                                  
                                                                                                                                                                                                                                                                                     500-MSE                                                                                                                              

   Legend:   → Mismatch (orange background)
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  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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1FKM)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GYP1_YEAST | Q084842g77

(-) Related Entries Specified in the PDB File

1ek0 GPPNHP-BOUND YPT51