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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GLYCOGENIN-1 (GYG1) COMPLEXED WITH MANGANESE, UDP-GLUCOSE AND GLUCOSE
 
Authors :  A. Chaikuad, D. S. Froese, E. Krysztofinska, F. Von Delft, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, C. Bountra, U. Oppermann, W. W. Yue, St Genomics Consortium (Sgc)
Date :  30 Jul 11  (Deposition) - 31 Aug 11  (Release) - 11 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Transferase, Glycosyltransferase, Glycogen Biosynthesis, Glycosylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Chaikuad, D. S. Froese, G. Berridge, F. Von Delft, U. Oppermann, W. W. Yue
Conformational Plasticity Of Glycogenin And Its Maltosaccharide Substrate During Glycogen Biogenesis.
Proc. Natl. Acad. Sci. Usa V. 108 21028 2011
PubMed-ID: 22160680  |  Reference-DOI: 10.1073/PNAS.1113921108

(-) Compounds

Molecule 1 - GLYCOGENIN-1
    Chains: A, B
    EC Number: 2.4.1.186
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)-R3-PRARE2
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: GLYCOGENIN (UNP RESIDUES 1-262)
    Gene: GYG, GYG1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GN-1, GN1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 24)

Asymmetric/Biological Unit (4, 24)
No.NameCountTypeFull Name
1EDO19Ligand/Ion1,2-ETHANEDIOL
2GLC1Ligand/IonALPHA-D-GLUCOSE
3MN2Ligand/IonMANGANESE (II) ION
4UPG2Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:77 , ASP A:125 , PRO A:126 , GLN A:164 , UPG A:265 , HOH A:414 , HOH A:482 , HOH A:500 , SER B:196BINDING SITE FOR RESIDUE GLC A 263
02AC2SOFTWAREASP A:102 , ASP A:104 , HIS A:212 , UPG A:265BINDING SITE FOR RESIDUE MN A 264
03AC3SOFTWARELEU A:9 , THR A:10 , THR A:11 , ASN A:12 , TYR A:15 , ARG A:77 , LEU A:80 , THR A:83 , LYS A:86 , ASP A:102 , ALA A:103 , ASP A:104 , ASN A:133 , SER A:134 , GLY A:135 , ASP A:160 , GLY A:162 , ASP A:163 , GLN A:164 , HIS A:212 , LEU A:214 , GLY A:215 , LYS A:218 , GLC A:263 , MN A:264BINDING SITE FOR RESIDUE UPG A 265
04AC4SOFTWARESER A:142 , VAL A:143 , GLU A:144BINDING SITE FOR RESIDUE EDO A 266
05AC5SOFTWAREASP A:178 , ILE A:179 , ILE B:179BINDING SITE FOR RESIDUE EDO A 267
06AC6SOFTWAREARG A:34 , ARG B:48BINDING SITE FOR RESIDUE EDO A 268
07AC7SOFTWAREGLU A:119 , LEU A:120 , SER A:173 , TRP A:174 , LYS A:181 , HOH A:280 , HOH A:305BINDING SITE FOR RESIDUE EDO A 269
08AC8SOFTWAREHIS A:29 , ASN A:110 , HOH A:300BINDING SITE FOR RESIDUE EDO A 270
09AC9SOFTWAREARG A:33BINDING SITE FOR RESIDUE EDO A 271
10BC1SOFTWARELYS A:97 , PHE A:115BINDING SITE FOR RESIDUE EDO A 272
11BC2SOFTWAREPHE A:171 , SER A:172 , SER A:173 , HOH A:370BINDING SITE FOR RESIDUE EDO A 273
12BC3SOFTWAREGLN A:28 , HIS A:29 , LEU A:108 , HOH A:333 , HOH A:510BINDING SITE FOR RESIDUE EDO A 274
13BC4SOFTWAREPRO A:41 , ARG A:48 , HOH A:471BINDING SITE FOR RESIDUE EDO A 275
14BC5SOFTWAREASP B:102 , ASP B:104 , HIS B:212 , UPG B:264BINDING SITE FOR RESIDUE MN B 263
15BC6SOFTWARELEU B:9 , THR B:10 , THR B:11 , ASN B:12 , TYR B:15 , ARG B:77 , LEU B:80 , THR B:83 , LYS B:86 , ASP B:102 , ALA B:103 , ASP B:104 , ASN B:133 , SER B:134 , GLY B:135 , ASP B:160 , GLY B:162 , ASP B:163 , GLN B:164 , HIS B:212 , GLY B:215 , LYS B:218 , MN B:263 , HOH B:319BINDING SITE FOR RESIDUE UPG B 264
16BC7SOFTWAREHIS B:29 , ARG B:30 , ASN B:110 , HOH B:325 , HOH B:466BINDING SITE FOR RESIDUE EDO B 265
17BC8SOFTWAREGLU B:119 , LEU B:120 , SER B:173 , TRP B:174 , LYS B:181 , HOH B:331BINDING SITE FOR RESIDUE EDO B 266
18BC9SOFTWARESER B:91 , GLN B:94 , HOH B:464 , HOH B:467BINDING SITE FOR RESIDUE EDO B 267
19CC1SOFTWAREARG B:34 , GLU B:57 , EDO B:269 , EDO B:273 , HOH B:465 , HOH B:555 , HOH B:577BINDING SITE FOR RESIDUE EDO B 268
20CC2SOFTWAREARG B:34 , EDO B:268BINDING SITE FOR RESIDUE EDO B 269
21CC3SOFTWARETHR B:93 , GLN B:94 , SER B:96 , HOH B:553BINDING SITE FOR RESIDUE EDO B 270
22CC4SOFTWAREVAL B:58 , HOH B:429BINDING SITE FOR RESIDUE EDO B 271
23CC5SOFTWAREHOH B:453BINDING SITE FOR RESIDUE EDO B 272
24CC6SOFTWAREGLU B:57 , GLN B:94 , EDO B:268 , HOH B:279 , HOH B:453 , HOH B:465 , HOH B:576BINDING SITE FOR RESIDUE EDO B 273

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T7O)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:119 -Leu A:120
2Glu B:119 -Leu B:120

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_072706A16PGLYG_HUMANDisease (PGBM2)  ---A/BA16P
2UniProtVAR_063768T83MGLYG_HUMANDisease (GSD15)267606858A/BT83M
3UniProtVAR_072707D102HGLYG_HUMANDisease (PGBM2)143137713A/BD102H
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T7O)

(-) Exons   (0, 0)

(no "Exon" information available for 3T7O)

(-) 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:263
 aligned with GLYG_HUMAN | P46976 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:263
                             1                                                                                                                                                                                                                                                                     
                             |       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   
           GLYG_HUMAN     - -MTDQAFVTLTTNDAYAKGALVLGSSLKQHRTTRRLVVLATPQVSDSMRKVLETVFDEVIMVDVLDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFDREELSAAPDPGWPDCFNSGVFVYQPSVETYNQLLHLASEQGSFDGGDQGILNTFFSSWATTDIRKHLPFIYNLSSISIYSYLPAFKVFGASAKVVHFLGRVKPWNYTYDPKTKSVKSEAHDPNMTHPEFLILWWNIFTTNVLPLLQ 262
               SCOP domains d3t7oa_ A: Glycogenin                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.....hhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------P------------------------------------------------------------------M------------------H---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t7o A   0 SMTDQAFVTLTTNDAYAKGALVLGSSLKQHRTTRRLVVLATPQVSDSMRKVLETVFDEVIMVDVLDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFDREELSAAPDPGWPDCFNSGVFVYQPSVETYNQLLHLASEQGSFDGGDQGILNTFFSSWATTDIRKHLPFIYNLSSISIYSYLPAFKVFGASAKVVHFLGRVKPWNYTYDPKTKSVKSEAHDPNMTHPEFLILWWNIFTTNVLPLLQ 262
                                     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   


Chain B from PDB  Type:PROTEIN  Length:263
 aligned with GLYG_HUMAN | P46976 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:263
                             1                                                                                                                                                                                                                                                                     
                             |       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   
           GLYG_HUMAN     - -MTDQAFVTLTTNDAYAKGALVLGSSLKQHRTTRRLVVLATPQVSDSMRKVLETVFDEVIMVDVLDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFDREELSAAPDPGWPDCFNSGVFVYQPSVETYNQLLHLASEQGSFDGGDQGILNTFFSSWATTDIRKHLPFIYNLSSISIYSYLPAFKVFGASAKVVHFLGRVKPWNYTYDPKTKSVKSEAHDPNMTHPEFLILWWNIFTTNVLPLLQ 262
               SCOP domains d3t7ob_ B: Glycogenin                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.hhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhh.eeee.......hhhhhhhh.hhhhhhhhhhhhhhhh....eeeee...eee...hhhhhhh...eeee.......eeeeeeee..hhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhh.hhhhheehhhhhhhhhhhhhhhhhh.eee.....hhhhheee....eee....hhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------P------------------------------------------------------------------M------------------H---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t7o B   0 SMTDQAFVTLTTNDAYAKGALVLGSSLKQHRTTRRLVVLATPQVSDSMRKVLETVFDEVIMVDVLDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFDREELSAAPDPGWPDCFNSGVFVYQPSVETYNQLLHLASEQGSFDGGDQGILNTFFSSWATTDIRKHLPFIYNLSSISIYSYLPAFKVFGASAKVVHFLGRVKPWNYTYDPKTKSVKSEAHDPNMTHPEFLILWWNIFTTNVLPLLQ 262
                                     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
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T7O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T7O)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GLYG_HUMAN | P46976)
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: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).
    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.
    GO:0005980    glycogen catabolic process    The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0043202    lysosomal lumen    The volume enclosed within the lysosomal membrane.
    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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  3t7o
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  GLYG_HUMAN | P46976
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 Related Entries

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

UniProtKB/Swiss-Prot
        GLYG_HUMAN | P46976: 3q4s 3qvb 3rmv 3rmw 3t7m 3t7n 3u2t 3u2u 3u2v 3u2w 3u2x

(-) Related Entries Specified in the PDB File

3q4s HGYG1 (Y195F) APO FORM
3qvb HGYG1 (Y195F) WITH UDP,MN IN OPEN FORM
3rmv HGYG1 (T83M) WITH UDP, MN
3rmw HGYG1 (T83M) WITH UDPG, MN
3t7m
3t7n