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Title :   CRYSTAL STRUCTURE OF A PUTATIVE UDP-GLUCOSE PYROPHOSPHORYLASE FROM ARABIDOPSIS THALIANA WITH BOUND UTP

Authors :   J. G. Mccoy, G. E. Wesenberg, G. N. Phillips Jr. , E. Bitto, C. A. Bingman, Center For Eukaryotic Structural Genomics (Cesg

Date :   13 Sep 06 (Deposition) - 26 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   At3G03250, Utp, Putative Udp-Glucose Pyrophosphorylase, Structural Genomics Functional Follow-Up Study, Structural Genomics, Protein Structure Initiative, Psi, Cesg, Center For Eukaryotic Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. G. Mccoy, E. Bitto, C. A. Bingman, G. E. Wesenberg, R. M. Bannen, D. A. Kondrashov, G. N. Phillips Jr.
Structure And Dynamics Of Udp-Glucose Pyrophosphorylase From Arabidopsis Thaliana With Bound Udp-Glucose And Utp.
J. Mol. Biol. V. 366 830 2007
PubMed-ID: 17178129 | Reference-DOI: 10.1016/J.JMB.2006.11.059
(for further references see the PDB file header)

Molecule 1 - PROBABLE UTP-GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE 2
	Chains	:	A, B
	EC Number	:	2.7.7.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVP-17
	Expression System Strain	:	B834 P(RARE2)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AT3G03250, T17B22.6
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	UDP-GLUCOSE PYROPHOSPHORYLASE 2, UDPGP 2, UGPASE 2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
2	UTP	2	Ligand/Ion	URIDINE 5'-TRIPHOSPHATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
2	UTP	1	Ligand/Ion	URIDINE 5'-TRIPHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	DMS	-1	Ligand/Ion	DIMETHYL SULFOXIDE
2	UTP	1	Ligand/Ion	URIDINE 5'-TRIPHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:353 , SER A:354 , PHE A:356 , ARG A:382 , PRO A:389 , ASN A:391 , HOH A:962 , HOH A:1111	BINDING SITE FOR RESIDUE DMS A 900
2	AC2	SOFTWARE	LEU A:85 , ASN A:86 , GLY A:87 , GLY A:88 , THR A:92 , LYS A:99 , GLN A:162 , PRO A:189 , GLY A:191 , HIS A:192 , ASN A:220 , SER A:221 , ASP A:222 , LYS A:360 , HOH A:1015 , HOH A:1030 , HOH A:1323 , HOH A:1325	BINDING SITE FOR RESIDUE UTP A 901
3	AC3	SOFTWARE	LEU B:85 , ASN B:86 , GLY B:87 , GLY B:88 , THR B:92 , LYS B:99 , MET B:134 , GLN B:162 , PRO B:189 , GLY B:191 , HIS B:192 , ASN B:220 , SER B:221 , ASP B:222 , LYS B:360 , HOH B:1024 , HOH B:1111 , HOH B:1135 , HOH B:1220	BINDING SITE FOR RESIDUE UTP B 902

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

(no "Cis Peptide Bond" information available for 2ICX)

(no "SAP(SNP)/Variant" information available for 2ICX)

(no "PROSITE Motif" information available for 2ICX)

(no "Exon" information available for 2ICX)

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:455
 aligned with UGPA2_ARATH | Q9M9P3 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:462
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467  
          UGPA2_ARATH     8 LPQLKSAVDGLTEMSESEKSGFISLVSRYLSGEAQHIEWSKIQTPTDEIVVPYEKMTPVSQDVAETKNLLDKLVVLKLNGGLGTTMGCTGPKSVIEVRDGLTFLDLIVIQIENLNNKYGCKVPLVLMNSFNTHDDTHKIVEKYTNSNVDIHTFNQSKYPRVVADEFVPWPSKGKTDKEGWYPPGHGDVFPALMNSGKLDTFLSQGKEYVFVANSDNLGAIVDLTILKHLIQNKNEYCMEVTPKTLADVKGGTLISYEGKVQLLEIAQVPDEHVNEFKSIEKFKIFNTNNLWVNLKAIKKLVEADALKMEIIPNPKEVDGVKVLQLETAAGAAIRFFDNAIGVNVPRSRFLPVKASSDLLLVQSDLYTLVDGFVTRNKARTNPSNPSIELGPEFKKVATFLSRFKSIPSIVELDSLKVSGDVWFGSSIVLKGKVTVAAKSGVKLEIPDRAVVENKNINGPEDL 469
               SCOP domains d2icxa2 A:8-383 UDP-glucose pyro     phosphorylase 2 (UDPGP 2)                                                                                                                                                                                                                                                                                                                          d2icxa1 A:384-469 UDP-glucose pyrophosphorylase 2 (UDPGP 2)                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh....hhhhhhhhhhhhhhhhhh-----hhhhh.......eee.hhh.....hhhhhhhhhh.eeeeeee...........hhhh.eee..eehhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh.....eeeee...ee.ee....ee.hhhh..hhh.ee..hhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhh..eeeeeee.....--..eeeee..eeeeehhhhhhhhhhhhhh......eeeeeeeeeehhhhhhhhhh...........eee..eeee....hhhhhhhhh...eeee.hhhhh....hhhhhhhhhh..eeee..eeee..........eeee.hhhhhhhhhhhh.........eeeeeee.eeee....eeeeeeeee.....eeee....eeeeeee.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2icx A   8 LPQLKSAVDGLTEMSESEKSGFISLVSRYLSG-----EWSKIQTPTDEIVVPYEKMTPVSQDVAETKNLLDKLVVLKLNGGLGTTMGCTGPKSVIEVRDGLTFLDLIVIQIENLNNKYGCKVPLVLMNSFNTHDDTHKIVEKYTNSNVDIHTFNQSKYPRVVADEFVPWPSKGKTDKEGWYPPGHGDVFPALMNSGKLDTFLSQGKEYVFVANSDNLGAIVDLTILKHLIQNKNEYCMEVTPKTLAD--GGTLISYEGKVQLLEIAQVPDEHVNEFKSIEKFKIFNTNNLWVNLKAIKKLVEADALKMEIIPNPKEVDGVKVLQLETAAGAAIRFFDNAIGVNVPRSRFLPVKASSDLLLVQSDLYTLVDGFVTRNKARTNPSNPSIELGPEFKKVATFLSRFKSIPSIVELDSLKVSGDVWFGSSIVLKGKVTVAAKSGVKLEIPDRAVVENKNINGPEDL 469
                                    17        27        37 |     |47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247      |257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467  
                                                          39    45                                                                                                                                                                                                              254  |                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                                   257

Chain B from PDB  Type:PROTEIN  Length:459
 aligned with UGPA2_ARATH | Q9M9P3 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:462
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467  
          UGPA2_ARATH     8 LPQLKSAVDGLTEMSESEKSGFISLVSRYLSGEAQHIEWSKIQTPTDEIVVPYEKMTPVSQDVAETKNLLDKLVVLKLNGGLGTTMGCTGPKSVIEVRDGLTFLDLIVIQIENLNNKYGCKVPLVLMNSFNTHDDTHKIVEKYTNSNVDIHTFNQSKYPRVVADEFVPWPSKGKTDKEGWYPPGHGDVFPALMNSGKLDTFLSQGKEYVFVANSDNLGAIVDLTILKHLIQNKNEYCMEVTPKTLADVKGGTLISYEGKVQLLEIAQVPDEHVNEFKSIEKFKIFNTNNLWVNLKAIKKLVEADALKMEIIPNPKEVDGVKVLQLETAAGAAIRFFDNAIGVNVPRSRFLPVKASSDLLLVQSDLYTLVDGFVTRNKARTNPSNPSIELGPEFKKVATFLSRFKSIPSIVELDSLKVSGDVWFGSSIVLKGKVTVAAKSGVKLEIPDRAVVENKNINGPEDL 469
               SCOP domains d2icxb2 B:8-383 UDP-glucose pyro  phosphorylase 2 (UDPGP 2)                                                                                                                                                                                                                                                                                                                             d2icxb1 B:384-469 UDP-glucose pyrophosphorylase 2 (UDPGP 2)                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh....hhhhhhhhhhhhhhhhhh--...hhhhh.......eee.hhh.....hhhhhhhhhh.eeeeee....hhhhh...hhhh.eee..eehhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh.....eeeee...ee.ee....ee.hhhh..hhh.ee..hhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhh..eeeeeee..-......eeeee..eeeeehhhhhhhhhhhhhh......eeeeeeeeeehhhhhhhhhh...........eee..eeee....hhhhhhhhh...eeee.hhhhh....hhhhhhhhhh..eeee..eeee..........eeee.hhhhhhhhhhhhh........eeeeeee.eeee....eeeeeeeee.....eeee....eeeeeee.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2icx B   8 LPQLKSAVDGLTEMSESEKSGFISLVSRYLSG--QHIEWSKIQTPTDEIVVPYEKMTPVSQDVAETKNLLDKLVVLKLNGGLGTTMGCTGPKSVIEVRDGLTFLDLIVIQIENLNNKYGCKVPLVLMNSFNTHDDTHKIVEKYTNSNVDIHTFNQSKYPRVVADEFVPWPSKGKTDKEGWYPPGHGDVFPALMNSGKLDTFLSQGKEYVFVANSDNLGAIVDLTILKHLIQNKNEYCMEVTPKT-ADVKGGTLISYEGKVQLLEIAQVPDEHVNEFKSIEKFKIFNTNNLWVNLKAIKKLVEADALKMEIIPNPKEVDGVKVLQLETAAGAAIRFFDNAIGVNVPRSRFLPVKASSDLLLVQSDLYTLVDGFVTRNKARTNPSNPSIELGPEFKKVATFLSRFKSIPSIVELDSLKVSGDVWFGSSIVLKGKVTVAAKSGVKLEIPDRAVVENKNINGPEDL 469
                                    17        27        37 |  |   47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247   | | 257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467  
                                                          39 42                                                                                                                                                                                                              251 |                                                                                                                                                                                                                        
                                                                                                                                                                                                                                                                               253

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 '\|'

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (UGPA2_ARATH | Q9M9P3)

molecular function
	GO:0003983	UTP:glucose-1-phosphate uridylyltransferase activity	Catalysis of the reaction: alpha-D-glucose 1-phosphate + UTP = diphosphate + UDP-D-glucose.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	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:0070569	uridylyltransferase activity	Catalysis of the transfer of an uridylyl group to an acceptor.
biological process
	GO:0006011	UDP-glucose metabolic process	The chemical reactions and pathways involving UDP-glucose, uridinediphosphoglucose, a substance composed of glucose in glycosidic linkage with uridine diphosphate.
	GO:0052543	callose deposition in cell wall	Any process in which callose is transported to, and/or maintained in, the cell wall. Callose is a linear 1,3-beta-d-glucan formed from UDP-glucose and is found in certain plant cell walls.
	GO:0016036	cellular response to phosphate starvation	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of phosphate.
	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:0009555	pollen development	The process whose specific outcome is the progression of the pollen grain over time, from its formation to the mature structure. The process begins with the meiosis of the microsporocyte to form four haploid microspores. The nucleus of each microspore then divides by mitosis to form a two-celled organism, the pollen grain, that contains a tube cell as well as a smaller generative cell. The pollen grain is surrounded by an elaborate cell wall. In some species, the generative cell immediately divides again to give a pair of sperm cells. In most flowering plants, however this division takes place later, in the tube that develops when a pollen grain germinates.
	GO:0009651	response to salt stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
	GO:0005985	sucrose metabolic process	The chemical reactions and pathways involving sucrose, the disaccharide fructofuranosyl-glucopyranoside.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0090406	pollen tube	A tubular cell projection that is part of a pollen tube cell and extends from a pollen grain.

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	UGPA2_ARATH \| Q9M9P3	:	1z90 2icy 2q4j

1z90	SAME PROTEIN WITHOUT SUBSTRATE
2icy	SAME PROTEIN WITH BOUND UDP-GLUCOSE RELATED ID: GO.14914 RELATED DB: TARGETDB

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