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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE UDP-GLUCOSE PYROPHOSPHORYLASE FROM ARABIDOPSIS THALIANA WITH BOUND UDP-GLUCOSE
 
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) - 03 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym. Unit :  A,B  (2x)
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  At3G03250, Udp, 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)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit (2x): AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2U5P1Ligand/IonURIDINE-5'-MONOPHOSPHATE
3UPG2Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
2U5P-1Ligand/IonURIDINE-5'-MONOPHOSPHATE
3UPG1Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1DMS-1Ligand/IonDIMETHYL SULFOXIDE
2U5P-1Ligand/IonURIDINE-5'-MONOPHOSPHATE
3UPG1Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:157 , HIS A:158 , THR A:159 , LYS A:204BINDING SITE FOR RESIDUE DMS A 900
2AC2SOFTWARELEU A:85 , GLY A:87 , GLY A:88 , MET A:134 , GLN A:162 , PRO A:189 , GLY A:191 , HIS A:192 , ASN A:220 , SER A:221 , ASN A:293 , THR A:294 , ASN A:295 , PHE A:356 , HOH A:927 , HOH A:962 , HOH A:1049 , HOH A:1138 , HOH A:1192BINDING SITE FOR RESIDUE UPG A 901
3AC3SOFTWAREALA B:14 , LEU B:18 , SER B:178BINDING SITE FOR RESIDUE HOH B 903

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ICY)

(-) 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:456
 aligned with UGPA2_ARATH | Q9M9P3 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:462
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464  
          UGPA2_ARATH     5 TENLPQLKSAVDGLTEMSESEKSGFISLVSRYLSGEAQHIEWSKIQTPTDEIVVPYEKMTPVSQDVAETKNLLDKLVVLKLNGGLGTTMGCTGPKSVIEVRDGLTFLDLIVIQIENLNNKYGCKVPLVLMNSFNTHDDTHKIVEKYTNSNVDIHTFNQSKYPRVVADEFVPWPSKGKTDKEGWYPPGHGDVFPALMNSGKLDTFLSQGKEYVFVANSDNLGAIVDLTILKHLIQNKNEYCMEVTPKTLADVKGGTLISYEGKVQLLEIAQVPDEHVNEFKSIEKFKIFNTNNLWVNLKAIKKLVEADALKMEIIPNPKEVDGVKVLQLETAAGAAIRFFDNAIGVNVPRSRFLPVKASSDLLLVQSDLYTLVDGFVTRNKARTNPSNPSIELGPEFKKVATFLSRFKSIPSIVELDSLKVSGDVWFGSSIVLKGKVTVAAKSGVKLEIPDRAVVENKNINGP 466
               SCOP domains d2icya2 A:5-383 UDP-glucose pyrop      hosphorylase 2 (UDPGP 2)                                                                                                                                                                                                                                                                                                                            d2icya1 A:384-466 UDP-glucose pyrophosphorylase 2 (UDPGP 2)                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...hhhhhhhhhhhhhhhh------.hhhhh.......eee.hhh.....hhhhhhhhhh.eeeeeee...hhhhh...hhhh.eee..eehhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh.....eeeee...ee.ee....ee.hhhh..hhh.ee..hhhhhhhhhhhhhhhhhhhh....eeeeee........hhhhhhhhhhhh..eeeeeee.........eeeee..eeeeehhhhhhhhhhhhhhh.....eeeeeeeeeehhhhhhhhhh..........eeee..eeee....hhhhhhhhh...eeee.hhhhh....hhhhhhhhhh..eeee..eeee..........eeee.hhhhhhhhhhhh.........eeeeeee.eeee....eeeeeeeee.....eeee....eee..ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2icy A   5 TENLPQLKSAVDGLTEMSESEKSGFISLVSRYL------IEWSKIQTPTDEIVVPYEKMTPVSQDVAETKNLLDKLVVLKLNGGLGTTMGCTGPKSVIEVRDGLTFLDLIVIQIENLNNKYGCKVPLVLMNSFNTHDDTHKIVEKYTNSNVDIHTFNQSKYPRVVADEFVPWPSKGKTDKEGWYPPGHGDVFPALMNSGKLDTFLSQGKEYVFVANSDNLGAIVDLTILKHLIQNKNEYCMEVTPKTLADVKGGTLISYEGKVQLLEIAQVPDEHVNEFKSIEKFKIFNTNNLWVNLKAIKKLVEADALKMEIIPNPKEVDGVKVLQLETAAGAAIRFFDNAIGVNVPRSRFLPVKASSDLLLVQSDLYTLVDGFVTRNKARTNPSNPSIELGPEFKKVATFLSRFKSIPSIVELDSLKVSGDVWFGSSIVLKGKVTVAAKSGVKLEIPDRAVVENKNINGP 466
                                    14        24        34  |     44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464  
                                                           37     44                                                                                                                                                                                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:463
 aligned with UGPA2_ARATH | Q9M9P3 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:463
                                    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       466   
          UGPA2_ARATH     7 NLPQLKSAVDGLTEMSESEKSGFISLVSRYLSGEAQHIEWSKIQTPTDEIVVPYEKMTPVSQDVAETKNLLDKLVVLKLNGGLGTTMGCTGPKSVIEVRDGLTFLDLIVIQIENLNNKYGCKVPLVLMNSFNTHDDTHKIVEKYTNSNVDIHTFNQSKYPRVVADEFVPWPSKGKTDKEGWYPPGHGDVFPALMNSGKLDTFLSQGKEYVFVANSDNLGAIVDLTILKHLIQNKNEYCMEVTPKTLADVKGGTLISYEGKVQLLEIAQVPDEHVNEFKSIEKFKIFNTNNLWVNLKAIKKLVEADALKMEIIPNPKEVDGVKVLQLETAAGAAIRFFDNAIGVNVPRSRFLPVKASSDLLLVQSDLYTLVDGFVTRNKARTNPSNPSIELGPEFKKVATFLSRFKSIPSIVELDSLKVSGDVWFGSSIVLKGKVTVAAKSGVKLEIPDRAVVENKNINGPEDL 469
               SCOP domains d2icyb2 B:7-383 UDP-glucose pyrophosphorylase 2 (UDPGP 2)                                                                                                                                                                                                                                                                                                                                d2icyb1 B:384-469 UDP-glucose pyrophosphorylase 2 (UDPGP 2)                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhh.......eee.hhh.....hhhhhhhhhh.eeeeee....hhhhh...hhhh.eee..eehhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh.....eeeee...ee.ee....ee.......hhh.ee..hhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhh..eeeeeee.hhhhh...eeeee..eeeeehhhhhhhhhhhhhh......eeeeeeeeeehhhhhhhhhh...........eee..eeee.....hhhhhhhh...eeee.hhhhh....hhhhhhhhhh..eeee..eeee..........eee.hhhhhhhhhhhhh.....eeeeeeeeeee.eeee....eeeeeeeee.....eeee....eeeeeee.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2icy B   7 NLPQLKSAVDGLTEMSESEKSGFISLVSRYLSGEAQHIEWSKIQTPTDEIVVPYEKMTPVSQDVAETKNLLDKLVVLKLNGGLGTTMGCTGPKSVIEVRDGLTFLDLIVIQIENLNNKYGCKVPLVLMNSFNTHDDTHKIVEKYTNSNVDIHTFNQSKYPRVVADEFVPWPSKGKTDKEGWYPPGHGDVFPALMNSGKLDTFLSQGKEYVFVANSDNLGAIVDLTILKHLIQNKNEYCMEVTPKTLADVKGGTLISYEGKVQLLEIAQVPDEHVNEFKSIEKFKIFNTNNLWVNLKAIKKLVEADALKMEIIPNPKEVDGVKVLQLETAAGAAIRFFDNAIGVNVPRSRFLPVKASSDLLLVQSDLYTLVDGFVTRNKARTNPSNPSIELGPEFKKVATFLSRFKSIPSIVELDSLKVSGDVWFGSSIVLKGKVTVAAKSGVKLEIPDRAVVENKNINGPEDL 469
                                    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       466
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

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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 Related Entries

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

UniProtKB/Swiss-Prot
        UGPA2_ARATH | Q9M9P3: 1z90 2icx 2q4j

(-) Related Entries Specified in the PDB File

1z90 NO SUBSTRATE BOUND
2icx SAME PROTEIN WITH BOUND UTP RELATED ID: GO.14914 RELATED DB: TARGETDB