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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ADP-GLUCOSE PHOSPHORYLASE FROM ARABIDOPSIS THALIANA WITH BOUND ADP-GLUCOSE
 
Authors :  J. G. Mccoy, G. E. Wesenberg, G. N. Phillips Jr. , E. Bitto, C. A. Bingman, Center For Eukaryotic Structural Genomics (Cesg
Date :  22 May 06  (Deposition) - 13 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym./Biol. Unit :  A,B
Keywords :  At5G18200, Adp-Glucose, Galt-Like, Structural Genomics Functional Follow-Up Study, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. G. Mccoy, G. E. Wesenberg, G. N. Phillips Jr. , E. Bitto, C. A. Bingman
Crystal Structure Of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana With Bound Adp-Glucose
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE GALACTOSE-1-PHOSPHATE URIDYL TRANSFERASE
    Chains: A, B
    EC Number: 2.7.7.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP-16
    Expression System Strain: BL834(DE3) P(RARE)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AT5G18200
    Mutation: YES
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: GAL-1-P URIDYLYLTRANSFERASE, UDP-GLUCOSE-HEXOSE-1- PHOSPHATE URIDYLYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ADQ2Ligand/IonADENOSINE-5'-DIPHOSPHATE-GLUCOSE
2CL2Ligand/IonCHLORIDE ION
3ZN4Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:63 , CYS A:66 , HIS A:133 , HIS A:184BINDING SITE FOR RESIDUE ZN A 352
2AC2SOFTWARECYS A:216 , CYS A:219 , HIS A:255 , HIS A:310BINDING SITE FOR RESIDUE ZN A 353
3AC3SOFTWARECYS B:63 , CYS B:66 , HIS B:133 , HIS B:184BINDING SITE FOR RESIDUE ZN B 352
4AC4SOFTWARECYS B:216 , CYS B:219 , HIS B:255 , HIS B:310BINDING SITE FOR RESIDUE ZN B 353
5AC5SOFTWAREPHE B:259 , HIS B:260 , THR B:296 , HOH B:611BINDING SITE FOR RESIDUE CL B 401
6AC6SOFTWAREPHE A:259 , HIS A:260 , THR A:296BINDING SITE FOR RESIDUE CL A 402
7AC7SOFTWAREPHE A:65 , GLU A:72 , CYS A:73 , ALA A:74 , ILE A:92 , GLU A:93 , ASN A:94 , LEU A:95 , TYR A:96 , PHE A:171 , ASN A:173 , GLY A:179 , ALA A:180 , SER A:181 , MET A:182 , GLN A:188 , HOH A:559 , HOH A:614 , HOH A:615 , HOH A:687 , HOH A:690 , ARG B:41 , ARG B:44 , GLY B:321 , GLY B:323 , GLY B:324 , PHE B:325 , GLU B:326 , ILE B:333 , HOH B:544BINDING SITE FOR RESIDUE ADQ A 506
8AC8SOFTWAREARG A:41 , ARG A:44 , GLY A:321 , GLY A:323 , GLY A:324 , PHE A:325 , GLU A:326 , PHE B:65 , GLU B:72 , CYS B:73 , ALA B:74 , ILE B:92 , GLU B:93 , ASN B:94 , LEU B:95 , TYR B:96 , ASN B:173 , GLY B:179 , ALA B:180 , SER B:181 , MET B:182 , GLN B:188 , HOH B:537 , HOH B:546 , HOH B:629 , HOH B:672BINDING SITE FOR RESIDUE ADQ B 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H39)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:80 -Pro A:81
2Val B:80 -Pro B:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H39)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2H39)

(-) Exons   (0, 0)

(no "Exon" information available for 2H39)

(-) Sequences/Alignments

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:308
 aligned with AGLUP_ARATH | Q9FK51 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:329
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341         
          AGLUP_ARATH    22 SPELRKDPVTNRWVIFSPARAKRPTDFKSKSPQNPNPKPSSCPFCIGREQECAPELFRVPDHDPNWKLRVIENLYPALSRNLETQSTQPETGTSRTIVGFGFHDVVIESPVHSIQLSDIDPVGIGDILIAYKKRINQIAQHDSINYIQVFKNQGASAGASMSHSHSQMMALPVVPPTVSSRLDGTKDYFEETGKCCLCEAKSKHFVIDESSHFVSVAPFAATYPFEIWIIPKDHSSHFHHLDDVKAVDLGGLLKLMLQKIAKQLNDPPYNYMIHTSPLKVTESQLPYTHWFLQIVPQLSGVGGFEIGTGCYINPVFPEDVAKVMREVSL 350
               SCOP domains -d2h39a1 A:23-195 Galactose             -1-phosphate uridylyltransferase                                                                                                      d2h39a2 A:196-350 Galactose-1-phosphate uridylyltransferase                                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeeee.hhhhhh....-------------.......hhhhh..eeeee........eeeee..............--------.eee...eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeehhhhh......eeeeeee...hhhhhhhhhhhhhhhhhhh.....hhhhhheeeee...eeeee.........eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee......hhhhhhhh..eeeeee.....hhhhhhhh..ee..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h39 A  22 SPELRKDPVTNRWVIFSPARAKRPTDF-------------SCPFCIGREQECAPELFRVPDHDPNWKLRVIENLYPALSRNLETQS--------RTIVGFGFHDVVIESPVHSIQLSDIDPVGIGDILIAYKKRINQIAQHDSINYIQVFKNQGASAGASMSHSGSQMMALPVVPPTVSSRLDGTKDYFEETGKCCLCEAKSKHFVIDESSHFVSVAPFAATYPFEIWIIPKDHSSHFHHLDDVKAVDLGGLLKLMLQKIAKQLNDPPYNYMIHTSPLKVTESQLPYTHWFLQIVPQLSGVGGFEIGTGCYINPVFPEDVAKVMREVSL 350
                                    31        41      |  -         -|       71        81        91       101     |   -    |  121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341         
                                                     48            62                                          107      116                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:313
 aligned with AGLUP_ARATH | Q9FK51 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:331
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 
          AGLUP_ARATH    21 QSPELRKDPVTNRWVIFSPARAKRPTDFKSKSPQNPNPKPSSCPFCIGREQECAPELFRVPDHDPNWKLRVIENLYPALSRNLETQSTQPETGTSRTIVGFGFHDVVIESPVHSIQLSDIDPVGIGDILIAYKKRINQIAQHDSINYIQVFKNQGASAGASMSHSHSQMMALPVVPPTVSSRLDGTKDYFEETGKCCLCEAKSKHFVIDESSHFVSVAPFAATYPFEIWIIPKDHSSHFHHLDDVKAVDLGGLLKLMLQKIAKQLNDPPYNYMIHTSPLKVTESQLPYTHWFLQIVPQLSGVGGFEIGTGCYINPVFPEDVAKVMREVSLT 351
               SCOP domains --d2h39b1 B:23-195 Galactose           -1-phosphate uridylyltransferase                                                                                                        d2h39b2 B:196-350 Galactose-1-phosphate uridylyltransferase                                                                                                - SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeeee.hhhhhh....-----------.........hhhhh..eeeee........eeeee......hhhhhhhhh-------.eee...eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeehhhhh......eeeeeee...hhhhhhhhhhhhhhhhhhh.....hhhhhheeeee...eeeee.........eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee......hhhhhhhh..eeeeee.....hhhhhhhh..ee..hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h39 B  21 QSPELRKDPVTNRWVIFSPARAKRPTDF-----------PSSCPFCIGREQECAPELFRVPDHDPNWKLRVIENLYPALSRNLETQST-------RTIVGFGFHDVVIESPVHSIQLSDIDPVGIGDILIAYKKRINQIAQHDSINYIQVFKNQGASAGASMSHSGSQMMALPVVPPTVSSRLDGTKDYFEETGKCCLCEAKSKHFVIDESSHFVSVAPFAATYPFEIWIIPKDHSSHFHHLDDVKAVDLGGLLKLMLQKIAKQLNDPPYNYMIHTSPLKVTESQLPYTHWFLQIVPQLSGVGGFEIGTGCYINPVFPEDVAKVMREVSLT 351
                                    30        40       | -        60        70        80        90       100       | -     | 120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 
                                                      48          60                                             108     116
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2H39)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H39)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AGLUP_ARATH | Q9FK51)
molecular function
    GO:0043531    ADP binding    Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
    GO:0008108    UDP-glucose:hexose-1-phosphate uridylyltransferase activity    Catalysis of the reaction: alpha-D-galactose 1-phosphate + UDP-D-glucose = alpha-D-glucose 1-phosphate + UDP-D-galactose.
    GO:0017103    UTP:galactose-1-phosphate uridylyltransferase activity    Catalysis of the reaction: alpha-D-galactose 1-phosphate + UTP = diphosphate + UDP-D-galactose.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0047345    ribose-5-phosphate adenylyltransferase activity    Catalysis of the reaction: D-ribose 5-phosphate + ADP + H(+) = ADP-ribose + phosphate.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006012    galactose metabolic process    The chemical reactions and pathways involving galactose, the aldohexose galacto-hexose. D-galactose is widely distributed in combined form in plants, animals and microorganisms as a constituent of oligo- and polysaccharides; it also occurs in galactolipids and as its glucoside in lactose and melibiose.
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    GO:0080040    positive regulation of cellular response to phosphate starvation    Any process that activates or increases the frequency, rate or extent of cellular response to phosphate starvation.

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  2h39
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 Related Entries

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

UniProtKB/Swiss-Prot
        AGLUP_ARATH | Q9FK51: 1z84 1zwj 2q4h 2q4l

(-) Related Entries Specified in the PDB File

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