3RMW - JenaLib

Title :   CRYSTAL STRUCTURE OF HUMAN GLYCOGENIN-1 (GYG1) T83M MUTANT COMPLEXED WITH MANGANESE AND UDP-GLUCOSE

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 :   21 Apr 11 (Deposition) - 11 May 11 (Release) - 11 Jan 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

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 (4, 15)

Sites (15, 15)

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:9 , THR A:10 , THR A:11 , ASN A:12 , TYR A:15 , 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 , MN A:264 , EDO A:270 , HOH A:309 , HOH A:343 , HOH A:352 , HOH A:399 , HOH A:400 , HOH A:404 , HOH A:405 , HOH A:461 , HOH A:466	BINDING SITE FOR RESIDUE UPG A 263
02	AC2	SOFTWARE	ASP A:102 , ASP A:104 , HIS A:212 , UPG A:263	BINDING SITE FOR RESIDUE MN A 264
03	AC3	SOFTWARE	ASP A:3 , GLN A:94 , HIS A:151 , GLU A:155 , HOH A:417 , HOH A:418	BINDING SITE FOR RESIDUE MG A 265
04	AC4	SOFTWARE	VAL A:61 , HIS A:88 , SER A:91 , LEU A:92 , HOH A:340	BINDING SITE FOR RESIDUE EDO A 266
05	AC5	SOFTWARE	THR A:93 , VAL A:143 , HOH A:293 , HOH A:446 , HOH A:447	BINDING SITE FOR RESIDUE EDO A 267
06	AC6	SOFTWARE	PRO A:124 , PRO A:129 , ASP A:130 , HIS A:182 , HOH A:348	BINDING SITE FOR RESIDUE EDO A 268
07	AC7	SOFTWARE	GLU A:119 , LEU A:120 , SER A:173 , TRP A:174 , LYS A:181 , HOH A:312	BINDING SITE FOR RESIDUE EDO A 269
08	AC8	SOFTWARE	VAL A:82 , LYS A:86 , GLY A:161 , ASP A:163 , UPG A:263	BINDING SITE FOR RESIDUE EDO A 270
09	AC9	SOFTWARE	THR A:2 , GLN A:94 , GLN A:148 , HIS A:151 , HOH A:334	BINDING SITE FOR RESIDUE EDO A 271
10	BC1	SOFTWARE	PHE A:170 , PHE A:171 , HOH A:283 , HOH A:356	BINDING SITE FOR RESIDUE EDO A 272
11	BC2	SOFTWARE	ASP A:56 , GLU A:57 , VAL A:58 , HOH A:436 , HOH A:438	BINDING SITE FOR RESIDUE EDO A 273
12	BC3	SOFTWARE	PRO A:41 , ASP A:62 , GLN A:262 , HOH A:336	BINDING SITE FOR RESIDUE EDO A 274
13	BC4	SOFTWARE	ASP A:45 , LYS A:49 , GLU A:52	BINDING SITE FOR RESIDUE EDO A 275
14	BC5	SOFTWARE	ASP A:65 , SER A:66 , HOH A:371	BINDING SITE FOR RESIDUE EDO A 276
15	BC6	SOFTWARE	ASP A:56 , GLU A:144 , HOH A:439	BINDING SITE FOR RESIDUE EDO A 277

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	M	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	M	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:250
 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 d3rmwa_ A: Glycogenin                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------Glyco_transf_8-3rmwA01 A:6-224                                                                                                                                                                                             ---------        --------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.hhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh.eeee.........hhhhhhhh..hhhhhhhhhhhhh....eeeee...eee...hhhhhhh...eeee.......eeeeeeee..hhhhhhhhhhhhhhhh.....hhhhhhhhh......hhhhh.hhhhh.....-----hhhhhhhhhh.eee.....hhhhh.ee....ee..--------.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------P------------------------------------------------------------------M------------------H---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rmw A   0 SMTDQAFVTLTTNDAYAKGALVLGSSLKQHRTTRRLVVLATPQVSDSMRKVLETVFDEVIMVDVLDSGDSAHLTLMKRPELGVMLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFDREELSAAPDPGWPDCFNSGVFVYQPSVETYNQLLHLASEQGSFDGGDQGILNTFFSSWATTDIRKHLPFIYNLSSIS-----PAFKVFGASAKVVHFLGRVKPWNYTYDPKTKSVKS--------HPEFLILWWNIFTTNVLPLLQ 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   
                                                                                                                                                                                                                           193   199                               233      242

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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