3QVB - JenaLib

Title :   CRYSTAL STRUCTURE OF HUMAN GLYCOGENIN-1 (GYG1) COMPLEXED WITH MANGANESE AND UDP

Authors :   A. Chaikuad, D. S. Froese, W. W. Yue, E. Krysztofinska, F. Von Delft, J. C. H. Arrowsmith, A. M. Edwards, C. Bountra, U. Oppermann, Structural Consortium (Sgc)

Date :   25 Feb 11 (Deposition) - 23 Mar 11 (Release) - 11 Jan 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.26

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:102 , ASP A:104 , HIS A:212 , UDP A:264	BINDING SITE FOR RESIDUE MN A 263
2	AC2	SOFTWARE	LEU A:9 , THR A:10 , THR A:11 , TYR A:15 , VAL A:82 , ASP A:102 , ALA A:103 , ASP A:104 , HIS A:212 , LEU A:214 , GLY A:215 , LYS A:218 , MN A:263 , HOH A:388	BINDING SITE FOR RESIDUE UDP A 264
3	AC3	SOFTWARE	HIS A:29 , ARG A:30 , ASN A:110	BINDING SITE FOR RESIDUE EDO A 265
4	AC4	SOFTWARE	THR A:93 , SER A:142 , VAL A:143 , GLU A:144	BINDING SITE FOR RESIDUE EDO A 266
5	AC5	SOFTWARE	GLU A:119 , LEU A:120 , SER A:173 , LYS A:181 , HOH A:364	BINDING SITE FOR RESIDUE EDO A 267
6	AC6	SOFTWARE	HIS A:88 , LEU A:92 , HOH A:308	BINDING SITE FOR RESIDUE EDO A 268
7	AC7	SOFTWARE	SER A:44 , ASP A:45 , SER A:46 , SER A:158 , PHE A:159 , ASP A:160 , GLY A:161	BINDING SITE FOR RESIDUE EDO A 269

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

Asymmetric Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_072706	A	16	P	GLYG_HUMAN	Disease (PGBM2)	---	A	A	16	P
2	UniProt	VAR_063768	T	83	M	GLYG_HUMAN	Disease (GSD15)	267606858	A	T	83	M
3	UniProt	VAR_072707	D	102	H	GLYG_HUMAN	Disease (PGBM2)	143137713	A	D	102	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_072706	A	16	P	GLYG_HUMAN	Disease (PGBM2)	---	A	A	16	P
2	UniProt	VAR_063768	T	83	M	GLYG_HUMAN	Disease (GSD15)	267606858	A	T	83	M
3	UniProt	VAR_072707	D	102	H	GLYG_HUMAN	Disease (PGBM2)	143137713	A	D	102	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:251
 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 d3qvba_ A: Glycogenin                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------Glyco_transf_8-3qvbA01 A:6-224                                                                                                                                                                                             ---------       ---------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.hhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhh....eeee.........hhhhhhhh..hhhhhhhhhhhhh....eeeee...eee...hhhhhhh...eeee.......eeeeeeee..hhhhhhhhhhhhhhhh....hhhhhhhhhh......hhhhh.hhhhhee..-----hhhhhhhhhhh.eee.....hhhhh.ee....ee..-------..hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------P------------------------------------------------------------------M------------------H---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qvb A   0 SMTDQAFVTLTTNDAYAKGALVLGSSLKQHRTTRRLVVLATPQVSDSMRKVLETVFDEVIMVDVLDSGDSAHLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFDREELSAAPDPGWPDCFNSGVFVYQPSVETYNQLLHLASEQGSFDGGDQGILNTFFSSWATTDIRKHLPFIYNLSSI-----LPAFKVFGASAKVVHFLGRVKPWNYTYDPKTKSVKS-------THPEFLILWWNIFTTNVLPLLQ 262
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189  |    199       209       219       229   |     - |     249       259   
                                                                                                                                                                                                                          192   198                                233     241

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, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A (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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	Cis Peptide Bonds
		Glu A:119 - Leu A:120	[ RasMol ]

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	3qvb
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	GLYG_HUMAN \| P46976
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	2.4.1.186
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