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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE AND ACTIVITY OF A FLAVONOID 3-O GLUCOSYLTRANSFERASE REVEALS THE BASIS FOR PLANT NATURAL PRODUCT MODIFICATION

Authors :   W. Offen, C. Martinez-Fleites, E. Kiat-Lim, M. Yang, B. G. Davis, C. A. Tarling, C. M. Ford, D. J. Bowles, G. J. Davies

Date :   22 Sep 05 (Deposition) - 09 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Glycosyltransferase, Flavonoid, Wine, Catalysis, Glycosylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Offen, C. Martinez-Fleites, M. Yang, E. Kiat-Lim, B. G. Davis, C. A. Tarling, C. M. Ford, D. J. Bowles, G. J. Davies
Structure Of A Flavonoid Glucosyltransferase Reveals The Basis For Plant Natural Product Modification.
Embo J. V. 25 1396 2006
PubMed-ID: 16482224 | Reference-DOI: 10.1038/SJ.EMBOJ.7600970

Molecule 1 - UDP-GLUCOSE FLAVONOID 3-O GLYCOSYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.4.1.91
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Organism Common	:	GRAPE
	Organism Scientific	:	VITIS VINIFERA
	Organism Taxid	:	29760

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	B3P	1	Ligand/Ion	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	UDP	1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:18 , THR A:19 , SER A:277 , THR A:280 , SER A:306 , TRP A:332 , ALA A:333 , GLN A:335 , HIS A:350 , GLY A:352 , TRP A:353 , ASN A:354 , SER A:355 , GLU A:358 , B3P A:1458 , HOH A:2227 , HOH A:2367 , HOH A:2368 , HOH A:2369	BINDING SITE FOR RESIDUE UDP A1457
2	AC2	SOFTWARE	SER A:18 , THR A:19 , HIS A:20 , GLN A:84 , ILE A:87 , THR A:141 , ALA A:142 , PHE A:200 , GLY A:352 , TRP A:353 , ASN A:354 , ASP A:374 , GLN A:375 , ASN A:378 , UDP A:1457 , HOH A:2001 , HOH A:2002 , HOH A:2370	BINDING SITE FOR RESIDUE B3P A1458

(no "SS Bond" information available for 2C1X)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:244	-	Pro A:245

Asymmetric/Biological Unit (16, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_UFOG_VITVI_001 *	Q	47	Z	UFOG_VITVI	---	---	A	Q	47	Z
02	UniProt	VAR_UFOG_VITVI_002 *	I	69	V	UFOG_VITVI	---	---	A	I	69	V
03	UniProt	VAR_UFOG_VITVI_003 *	P	74	A	UFOG_VITVI	---	---	A	P	74	A
04	UniProt	VAR_UFOG_VITVI_004 *	T	91	M	UFOG_VITVI	---	---	A	T	91	M
05	UniProt	VAR_UFOG_VITVI_005 *	L	134	V	UFOG_VITVI	---	---	A	V	134	V
06	UniProt	VAR_UFOG_VITVI_006 *	I	153	T	UFOG_VITVI	---	---	A	I	153	T
07	UniProt	VAR_UFOG_VITVI_007 *	G	161	A	UFOG_VITVI	---	---	A	G	161	A
08	UniProt	VAR_UFOG_VITVI_009 *	V	289	L	UFOG_VITVI	---	---	A	V	289	L
09	UniProt	VAR_UFOG_VITVI_010 *	S	293	A	UFOG_VITVI	---	---	A	S	293	A
10	UniProt	VAR_UFOG_VITVI_011 *	R	312	S	UFOG_VITVI	---	---	A	R	312	S
11	UniProt	VAR_UFOG_VITVI_012 *	Y	326	H	UFOG_VITVI	---	---	A	Y	326	H
12	UniProt	VAR_UFOG_VITVI_013 *	F	372	Y	UFOG_VITVI	---	---	A	F	372	Y
13	UniProt	VAR_UFOG_VITVI_014 *	V	385	A	UFOG_VITVI	---	---	A	V	385	A
14	UniProt	VAR_UFOG_VITVI_015 *	K	399	E	UFOG_VITVI	---	---	A	K	399	E
15	UniProt	VAR_UFOG_VITVI_016 *	R	423	G	UFOG_VITVI	---	---	A	R	423	G
16	UniProt	VAR_UFOG_VITVI_017 *	I	444	K	UFOG_VITVI	---	---	A	I	444	K
	* ID not provided by source

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UDPGT	PS00375	UDP-glycosyltransferases signature.	UFOG_VITVI	332-375	1	A:332-375

(no "Exon" information available for 2C1X)

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:434
 aligned with UFOG_VITVI | P51094 from UniProtKB/Swiss-Prot  Length:456

    Alignment length:450
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456
           UFOG_VITVI     7 NPHVAVLAFPFSTHAAPLLAVVRRLAAAAPHAVFSFFSTSQSNASIFHDSMHTMQCNIKSYDISDGVPEGYVFAGRPQEDIELFTRAAPESFRQGMVMAVAETGRPVSCLVADAFIWFAADMAAEMGLAWLPFWTAGPNSLSTHVYIDEIREKIGVSGIQGREDELLNFIPGMSKVRFRDLQEGIVFGNLNSLFSRMLHRMGQVLPKATAVFINSFEELDDSLTNDLKSKLKTYLNIGPFNLITPPPVVPNTTGCLQWLKERKPTSVVYISFGTVTTPPPAEVVALSEALEASRVPFIWSLRDKARVHLPEGFLEKTRGYGMVVPWAPQAEVLAHEAVGAFVTHCGWNSLWESVAGGVPLICRPFFGDQRLNGRMVEDVLEIGVRIEGGVFTKSGLMSCFDQILSQEKGKKLRENLRALRETADRAVGPKGSSTENFITLVDLVSKPKDV 456
               SCOP domains d2c1xa1 A:7-456 UDP glucose:flavonoid 3-o-gluco       syltransferase                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhhhhhh...eeeeeehhhhhhhhh-------...eeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhhhhh......................hhhh..........hhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhh..eee..hhhhhh---------hhhhhhhh.....eeeee.......hhhhhhhhhhhhhhhh..eeee.hhhhhhhh..hhhhhhh..eeee...hhhhhhh...eeeeee..hhhhhhhhhhhh..eee.....hhhhhhhhhhhh...eee.hhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------Z---------------------V----A----------------M------------------------------------------V------------------T-------A-------------------------------------------------------------------------------------------------------------------------------L---A------------------S-------------H---------------------------------------------Y------------A-------------E-----------------------G--------------------K------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UDPGT  PDB: A:332-375 UniProt: 332-375      --------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2c1x A   7 NPHVAVLAFPFSTHAAPLLAVVRRLAAAAPHAVFSFFSTSQSNASIF-------QCNIKSYDISDGVPEGYVFAGRPQEDIELFTRAAPESFRQGMVMAVAETGRPVSCLVADAFIWFAADMAAEMGVAWLPFWTAGPNSLSTHVYIDEIREKIGVSGIQGREDELLNFIPGMSKVRFRDLQEGIVFGNLNSLFSRMLHRMGQVLPKATAVFINSFEELDDSLTNDLKSKLKTYLNIGPFNLIT---------GCLQWLKERKPTSVVYISFGTVTTPPPAEVVALSEALEASRVPFIWSLRDKARVHLPEGFLEKTRGYGMVVPWAPQAEVLAHEAVGAFVTHCGWNSLWESVAGGVPLICRPFFGDQRLNGRMVEDVLEIGVRIEGGVFTKSGLMSCFDQILSQEKGKKLRENLRALRETADRAVGPKGSSTENFITLVDLVSKPKDV 456
                                    16        26        36        46      |  -    |   66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246   |     -   |   266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456
                                                                         53      61                                                                                                                                                                                          250       260

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: UDP-Glycosyltransferase/glycogen phosphorylase (296)

Superfamily: UDP-Glycosyltransferase/glycogen phosphorylase (296)

Family: UDPGT-like (10)

Protein domain: UDP glucose:flavonoid 3-o-glucosyltransferase (1)

Grape (Vitis vinifera) [TaxId: 29760] (1)

d2c1xa1

A:7-456

(no "CATH Domain" information available for 2C1X)

(no "Pfam Domain" information available for 2C1X)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (UFOG_VITVI | P51094)

molecular function
	GO:0047213	anthocyanidin 3-O-glucosyltransferase activity	Catalysis of the reaction: anthocyanidin + UDP-D-glucose = anthocyanidin-3-O-D-glucoside + UDP.
	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).
	GO:0016758	transferase activity, transferring hexosyl groups	Catalysis of the transfer of a hexosyl group from one compound (donor) to another (acceptor).
biological process
	GO:0009718	anthocyanin-containing compound biosynthetic process	The chemical reactions and pathways resulting in the formation of anthocyanins, any member of a group of intensely colored soluble glycosides of anthocyanidins.
	GO:0033485	cyanidin 3-O-glucoside biosynthetic process	The chemical reactions and pathways resulting in the formation of cyanidin 3-O-glucoside, a basic anthocyanin responsible for red to magenta coloration of flowers and fruits.
	GO:0033330	kaempferol O-glucoside biosynthetic process	The chemical reactions and pathways leading to the formation of O-glucosylated derivatives of kaempferol.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0033303	quercetin O-glucoside biosynthetic process	The chemical reactions and pathways leading to the formation of O-glucosylated derivatives of quercetin.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:244 - Pro A:245	[ RasMol ]

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	2c1x
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	2.4.1.91
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	UFOG_VITVI \| P51094	:	2c1z 2c9z

2c1z	STRUCTURE AND ACTIVITY OF A FLAVONOID 3-O GLUCOSYLTRANFERASE REVEALS THE BASIS FOR PLANT NATURAL PRODUCT MODIFICATION
2c9z	STRUCTURE AND ACTIVITY OF A FLAVONOID 3-0 GLUCOSYLTRANSFERASE REVEALS THE BASIS FOR PLANT NATURAL PRODUCT MODIFICATION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (16, 16)

PROSITE Motifs (1, 1)

Exons (0, 0)

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SCOP Domains (1, 1)

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Gene Ontology (9, 9)

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