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(-) Description

Title :  SER162 MUTANT OF GLYCOGENIN COMPLEXED WITH UDP-GLUCOSE AND MANGANESE
 
Authors :  T. D. Hurley, S. L. Stout, E. Miner, J. Zhou, P. J. Roach
Date :  14 Apr 05  (Deposition) - 26 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Glycosyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. D. Hurley, S. Stout, E. Miner, J. Zhou, P. J. Roach
Requirements For Catalysis In Mammalian Glycogenin.
J. Biol. Chem. V. 280 23892 2005
PubMed-ID: 15849187  |  Reference-DOI: 10.1074/JBC.M502344200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCOGENIN-1
    Chains: A
    EC Number: 2.4.1.186
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET15B
    Expression System Strain: BL 21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: GYG, GYG1
    Mutation: YES
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1MN1Ligand/IonMANGANESE (II) ION
2SO41Ligand/IonSULFATE ION
3UPG1Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2SO42Ligand/IonSULFATE ION
3UPG2Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:101 , ASP A:103 , HIS A:211 , UPG A:411BINDING SITE FOR RESIDUE MN A 400
2AC2SOFTWAREASP A:177 , ILE A:178 , HOH A:437BINDING SITE FOR RESIDUE SO4 A 401
3AC3SOFTWARELEU A:8 , THR A:9 , THR A:10 , ASN A:11 , TYR A:14 , LYS A:85 , ASP A:101 , ALA A:102 , ASP A:103 , ASP A:124 , ASN A:132 , SER A:133 , GLY A:134 , GLN A:163 , HIS A:211 , LEU A:213 , LYS A:217 , MN A:400 , HOH A:485BINDING SITE FOR RESIDUE UPG A 411

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:118 -Leu A:119

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZDF)

(-) 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:258
 aligned with GLYG_RABIT | P13280 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:264
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
           GLYG_RABIT     1 MTDQAFVTLTTNDAYAKGALVLGSSLKQHRTSRRLAVLTTPQVSDTMRKALEIVFDEVITVDILDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFEREELSAAPDPGWPDCFNSGVFVYQPSVETYNQLLHVASEQGSFDGGDQGLLNTFFNSWATTDIRKHLPFIYNLSSISIYSYLPAFKAFGANAKVVHFLGQTKPWNYTYDTKTKSVRSEGHDPTMTHPQFLNVWWDIFTTSVVPLLQQF 264
               SCOP domains d1zdfa_ A: Glycogenin                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1zdfA00 A:0-263 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                             CATH domains
               Pfam domains -----Glyco_transf_8-1zdfA01 A:5-223                                                                                                                                                                                             ---------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhh.eeee.........hhhhhhhh..hhhhhhhhhhhhh....eeeee...eee...hhhhhhh...eeee.......eeeeeeee..hhhhhhhhhhhhhhh.....hhhhhhhhhh......hhhhh.hhhhheehhhhhhhhhhhhhhhhhh.eee.....hhhhh.ee....ee..------...hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zdf A   0 MTDQAFVTLTTNDAYAKGALVLGSSLKQHRTSRRLAVLTTPQVSDTMRKALEIVFDEVITVDILDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFEREELSAAPDPGWPDCFNSGVFVYQPSVETYNQLLHVASEQGSFDGGSQGLLNTFFNSWATTDIRKHLPFIYNLSSISIYSYLPAFKAFGANAKVVHFLGQTKPWNYTYDTKTKSVRS------MTHPQFLNVWWDIFTTSVVPLLQQF 263
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229  |    239       249       259    
                                                                                                                                                                                                                                                                  232    239
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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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (GLYG_RABIT | P13280)
molecular function
    GO:0008466    glycogenin glucosyltransferase activity    Catalysis of the reaction: UDP-glucose + glycogenin = UDP + glucosylglycogenin.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0005978    glycogen biosynthetic process    The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.

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  2.4.1.186
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 Related Entries

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

UniProtKB/Swiss-Prot
        GLYG_RABIT | P13280: 1ll0 1ll2 1ll3 1zct 1zcu 1zcv 1zcy 1zdg 3usq 3usr 3v8y 3v8z 3v90 3v91

(-) Related Entries Specified in the PDB File

1ll2 1ll3 1zct 1zcu 1zcv 1zcy 1zdg