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(-) Description

Title :  CRYSTAL STRUCTURE OF RABBIT MUSCLE GLYCOGENIN COMPLEXED WITH UDP-GLUCOSE AND MANGANESE
 
Authors :  B. J. Gibbons, P. J. Roach, T. D. Hurley
Date :  26 Apr 02  (Deposition) - 15 May 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Protein-Substrate Complex, Beta-Alpha-Beta Rossman-Like Nucleotide Binding Fold, Dxd Motif, Non-Proline Cis Peptide Bond, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. J. Gibbons, P. J. Roach, T. D. Hurley
Crystal Structure Of The Autocatalytic Initiator Of Glycoge Biosynthesis, Glycogenin.
J. Mol. Biol. V. 319 463 2002
PubMed-ID: 12051921  |  Reference-DOI: 10.1016/S0022-2836(02)00305-4

(-) Compounds

Molecule 1 - GLYCOGENIN-1
    Chains: A
    EC Number: 2.4.1.186
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21/DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Tissue: SKELETAL MUSCLE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:102 , ASP A:104 , HIS A:212 , UPG A:334BINDING SITE FOR RESIDUE MN A 333
2AC2SOFTWARELEU A:9 , THR A:10 , THR A:11 , ASN A:12 , TYR A:15 , ASP A:102 , ALA A:103 , ASP A:104 , ASP A:125 , ASN A:133 , SER A:134 , GLN A:164 , HIS A:212 , LEU A:214 , GLY A:215 , LYS A:218 , MN A:333 , HOH A:356 , HOH A:375 , HOH A:416 , HOH A:459 , HOH A:492 , HOH A:493 , HOH A:520 , HOH A:582BINDING SITE FOR RESIDUE UPG A 334

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LL2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:119 -Leu A:120

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LL2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LL2)

(-) Exons   (0, 0)

(no "Exon" information available for 1LL2)

(-) 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:255
 aligned with GLYG_RABIT | P13280 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:263
                                    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 MTDQAFVTLTTNDAYAKGALVLGSSLKQHRTSRRLAVLTTPQVSDTMRKALEIVFDEVITVDILDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFEREELSAAPDPGWPDCFNSGVFVYQPSVETYNQLLHVASEQGSFDGGDQGLLNTFFNSWATTDIRKHLPFIYNLSSISIYSYLPAFKAFGANAKVVHFLGQTKPWNYTYDTKTKSVRSEGHDPTMTHPQFLNVWWDIFTTSVVPLLQQ 263
               SCOP domains d1ll2a_ A: Glycogenin                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1ll2A00 A:1-262 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                            CATH domains
               Pfam domains -----Glyco_transf_8-1ll2A01 A:6-224                                                                                                                                                                                             --------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhh.eeee.........hhhhhhhh..hhhhhhhhhhhhh....eeeee...eee...hhhhhhh...eeee.......eeeeeeee..hhhhhhhhhhhhhhh.....hhhhhhhhhh......hhhhh.hhhhhee.hhhhhhhhhhhhhhhhh.eee.....hhhhh.ee....ee.--------.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ll2 A   1 MTDQAFVTLTTNDAYAKGALVLGSSLKQHRTSRRLAVLTTPQVSDTMRKALEIVFDEVITVDILDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFEREELSAAPDPGWPDCFNSGVFVYQPSVETYNQLLHVASEQGSFDGGDQGLLNTFFNSWATTDIRKHLPFIYNLSSISIYSYLPAFKAFGANAKVVHFLGQTKPWNYTYDTKTKSVR--------THPQFLNVWWDIFTTSVVPLLQQ 262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 |       -|      249       259   
                                                                                                                                                                                                                                                                 232      240
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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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  1ll2
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  GLYG_RABIT | P13280
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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 1ll3 1zct 1zcu 1zcv 1zcy 1zdf 1zdg 3usq 3usr 3v8y 3v8z 3v90 3v91

(-) Related Entries Specified in the PDB File

1ll0 PDB ID 1LL0 IS THE ORIGINAL 3.4A MAD STRUCTURE SOLUTION OF GLYCOGENIN WITH A PENTAMER OF DIMERS IN THE ASYMMETRIC UNIT AND P4(3)2(1)2 SPACE GROUP.
1ll3 PDB ID 1LL3 IS A 1.9A APO- ENZYME STRUCTURE OF GLYCOGENIN; I222 SPACE GROUP.