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(-) Description

Title :  CRYSTAL STRUCTURE OF POFUT1 IN COMPLEX WITH GDP-FUCOSE (CRYSTAL-FORM-II)
 
Authors :  E. Lira-Navarrete, J. Valero-Gonzalez, R. Villanueva, M. Martinez-J T. Tejero, P. Merino, S. Panjikar, R. Hurtado-Guerrero
Date :  17 Aug 11  (Deposition) - 14 Sep 11  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Glycosyltransferase, Gt-B, Catalytic Mechanism, Gt65 (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Lira-Navarrete, J. Valero-Gonzalez, R. Villanueva, M. Martinez-Julvez, T. Tejero, P. Merino, S. Panjikar, R. Hurtado-Guerrero
Structural Insights Into The Mechanism Of Protein O-Fucosylation.
Plos One V. 6 25365 2011
PubMed-ID: 21966509  |  Reference-DOI: 10.1371/JOURNAL.PONE.0025365

(-) Compounds

Molecule 1 - PUTATIVE GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1
    ChainsA
    EC Number2.4.1.221
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System StrainX-33
    Expression System Taxid4922
    FragmentRESIDUES 26-383
    Organism ScientificCAENORHABDITIS ELEGANS
    Organism Taxid6239
    SynonymPEPTIDE-O-FUCOSYLTRANSFERASE 1, O-FUCT-1, POFUT1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GFB1Ligand/IonGUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GFB2Ligand/IonGUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:39 , ARG A:40 , PHE A:41 , GLY A:42 , ASN A:43 , PRO A:133 , HIS A:238 , ARG A:240 , TRP A:245 , VAL A:248 , ALA A:307 , SER A:308 , ASP A:309 , ASP A:334 , MET A:336 , SER A:355 , THR A:356 , PHE A:357 , HOH A:2008 , HOH A:2011 , HOH A:2212BINDING SITE FOR RESIDUE GFB A1381

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:35 -A:37
2A:119 -A:135
3A:249 -A:281
4A:266 -A:353

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:141 -Pro A:142
2Phe A:199 -Pro A:200
3Lys A:232 -Pro A:233
4Glu A:332 -Pro A:333

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZY6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZY6)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZY6)

(-) Sequences/Alignments

Asymmetric 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:350
 aligned with OFUT1_CAEEL | Q18014 from UniProtKB/Swiss-Prot  Length:389

    Alignment length:356
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374      
          OFUT1_CAEEL    25 ETDPNGYIVFCPCMGRFGNQVDQFLGVLAFAKALDRTLVLPNFIEFKHPETKMIPFEFLFQVGTVAKYTRVVTMQEFTKKIMPTVWPPEKRKAFCWTPRQAIYDKSAEPGCHSKEGNPFGPYWDQIDVSFVGDEYFGDIPGGFDLNQMGSRKKWLEKFPSEEYPVLAFSSAPAPFPSKGKVWSIQKYLRWSSRITEQAKKFISANLAKPFVAVHLRNDADWVRVCEHIDTTTNRPLFASEQCLGEGHHLGTLTKEICSPSKQQILEQIVEKVGSIGAKSVFVASDKDHMIDEINEALKPYEIEAHRQEPDDMYTSLAIMGRADLFVGNCVSTFSHIVKRERDHAGQSPRPSAFFGI 380
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee.....hhhhhhhhhhhhhhhhhhhh.eee...eee......eeehhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhh.eeee......------..........hhhhhhhhh.....eeee..............hhhhhhhhh......eeee.........hhhhhhhhhhh..hhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhh...........hhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh..ee.....hhhhhhhhhhh..eeee...hhhhhhhhhhhhhh......eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zy6 A  25 ATDPNGYIVFCPCMGRFGNQVDQFLGVLAFAKALDRTLVLPNFIEFKHPETKMIPFEFLFQVGTVAKYTRVVTMQEFTKKIMPTVWPPEKRKAFCWTPRQA------EPGCHSKEGNPFGPYWDQIDVSFVGDEYFGDIPGGFDLNQMGSRKKWLEKFPSEEYPVLAFSSAPAPFPSKGKVWSIQKYLRWSSRITEQAKKFISANLAKPFVAVHLRNDADWVRVCEHIDTTTNRPLFASEQCLGEGHHLGTLTKEICSPSKQQILEQIVEKVGSIGAKSVFVASDKDHMIDEINEALKPYEIEAHRQEPDDMYTSLAIMGRADLFVGNCVSTFSHIVKRERDHAGQSPRPSAFFGI 380
                                    34        44        54        64        74        84        94       104       114       124|      134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374      
                                                                                                                              125    132                                                                                                                                                                                                                                                        

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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  (0, 0)

(no "SCOP Domain" information available for 3ZY6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZY6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZY6)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (OFUT1_CAEEL | Q18014)
molecular function
    GO:0008417    fucosyltransferase activity    Catalysis of the transfer of a fucosyl group to an acceptor molecule, typically another carbohydrate or a lipid.
    GO:0046922    peptide-O-fucosyltransferase activity    Catalysis of the transfer of an alpha-L-fucosyl residue from GDP- beta-L-fucose to the serine hydroxy group of a protein acceptor.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0007219    Notch signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006004    fucose metabolic process    The chemical reactions and pathways involving fucose, or 6-deoxygalactose, which has two enantiomers, D-fucose and L-fucose.
    GO:0036066    protein O-linked fucosylation    The process of transferring a fucosyl group to a serine or threonine residues in a protein acceptor molecule, to form an O-linked protein-sugar linkage.
    GO:0006493    protein O-linked glycosylation    A protein glycosylation process in which a carbohydrate or carbohydrate derivative unit is added to a protein via the hydroxyl group of peptidyl-serine, peptidyl-threonine, peptidyl-hydroxylysine, or peptidyl-hydroxyproline, or via the phenol group of peptidyl-tyrosine, forming an O-glycan.
    GO:0006486    protein glycosylation    A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins.
cellular component
    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).

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 Related Entries

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

UniProtKB/Swiss-Prot
        OFUT1_CAEEL | Q180143zy2 3zy3 3zy4 3zy5

(-) Related Entries Specified in the PDB File

3zy2 CRYSTAL STRUCTURE OF POFUT1 IN COMPLEX WITH GDP (HIGH RESOLUTION DATASET)
3zy3 CRYSTAL STRUCTURE OF POFUT1 IN COMPLEX WITH GDP ( CRYSTAL-FORM-III)
3zy4 CRYSTAL STRUCTURE OF POFUT1 APO-FORM (CRYSTAL-FORM-I)
3zy5 CRYSTAL STRUCTURE OF POFUT1 IN COMPLEX WITH GDP-FUCOSE (CRYSTAL-FORM-I)