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(-) Description

Title :  ENSEMBLE REFINEMENT OF THE CRYSTAL STRUCTURE OF GALT-LIKE PROTEIN FROM ARABIDOPSIS THALIANA AT5G18200
 
Authors :  E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips Jr. , Cent Eukaryotic Structural Genomics (Cesg)
Date :  31 May 07  (Deposition) - 19 Jun 07  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B  (4x)
Biol. Unit 1:  A,B  (1x)
Keywords :  Ensemble Refinement, Refinement Methodology Development, Galt, At5G18200, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips
Ensemble Refinement Of Protein Crystal Structures: Validation And Application.
Structure V. 15 1040 2007
PubMed-ID: 17850744  |  Reference-DOI: 10.1016/J.STR.2007.06.019
(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: PVP13
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AT5G18200, MRG7_16
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Strain: CV. COLUMBIA
    Synonym: GAL-1-P URIDYLYLTRANSFERASE, UDP-GLUCOSE-HEXOSE-1-PHOSPHATE URIDYLYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit (4x): AB
Biological Unit 1 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:63 , PHE A:65 , CYS A:66 , HIS A:133 , HIS A:184BINDING SITE FOR RESIDUE ZN A 400
2AC2SOFTWARECYS A:216 , CYS A:219 , HIS A:255 , HIS A:310BINDING SITE FOR RESIDUE ZN A 401
3AC3SOFTWARECYS B:63 , CYS B:66 , HIS B:133 , HIS B:184BINDING SITE FOR RESIDUE ZN B 402
4AC4SOFTWARECYS B:216 , CYS B:219 , HIS B:255 , HIS B:310BINDING SITE FOR RESIDUE ZN B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q4L)

(-) Cis Peptide Bonds  (2, 8)

Asymmetric Unit
No.ModelResidues
11, 2, 3, 4Val A:80 -Pro A:81
21, 2, 3, 4Val B:80 -Pro B:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q4L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q4L)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q4L)

(-) 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:301
 aligned with AGLUP_ARATH | Q9FK51 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:329
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342         
          AGLUP_ARATH    23 PELRKDPVTNRWVIFSPARAKRPTDFKSKSPQNPNPKPSSCPFCIGREQECAPELFRVPDHDPNWKLRVIENLYPALSRNLETQSTQPETGTSRTIVGFGFHDVVIESPVHSIQLSDIDPVGIGDILIAYKKRINQIAQHDSINYIQVFKNQGASAGASMSHSHSQMMALPVVPPTVSSRLDGTKDYFEETGKCCLCEAKSKHFVIDESSHFVSVAPFAATYPFEIWIIPKDHSSHFHHLDDVKAVDLGGLLKLMLQKIAKQLNDPPYNYMIHTSPLKVTESQLPYTHWFLQIVPQLSGVGGFEIGTGCYINPVFPEDVAKVMREVSLT 351
               SCOP domains d2q4la1 A:23-195         Gala          ctose-1-phosphate uridylyltransferase                                                                                                 d2q4la2 A:196-351 Galactose-1-phosphate uridylyltransferase                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeee..--------....----------..............eeeee........eeee.......hhhhh.----------.eee....eeeee............hhhhhhhhhhhhhhhhhhhh......eeeeeeeehhhhh......eeeeeee...hhhhhhhhhhhhhhhhhhh.hhhhhhhhh.eeeee...eeeee.........eeeee..........hhhhhhhhhhhhhhhhhhhhhhh....eeeeee......hhhhh.....eeeeee.....hhhhhhhh..ee...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q4l A  23 PELRKDPVTNRWVIFSP--------FKSK----------SCPFCIGREQECAPELFRVPDHDPNWKLRVIENLYPALSRNLET----------RTIVGFGFHDVVIESPVHSIQLSDIDPVGIGDILIAYKKRINQIAQHDSINYIQVFKNQGASAGASMSHSHSQMMALPVVPPTVSSRLDGTKDYFEETGKCCLCEAKSKHFVIDESSHFVSVAPFAATYPFEIWIIPKDHSSHFHHLDDVKAVDLGGLLKLMLQKIAKQLNDPPYNYMIHTSPLKVTESQLPYTHWFLQIVPQLSGVGGFEIGTGCYINPVFPEDVAKVMREVSLT 351
                                    32      |  -     |  |-        62        72        82        92       102  |      -   |   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342         
                                           39       48 51         62                                        105        116                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:299
 aligned with AGLUP_ARATH | Q9FK51 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:330
                                    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 QSPELRKDPVTNRWVIFSPARAKRPTDFKSKSPQNPNPKPSSCPFCIGREQECAPELFRVPDHDPNWKLRVIENLYPALSRNLETQSTQPETGTSRTIVGFGFHDVVIESPVHSIQLSDIDPVGIGDILIAYKKRINQIAQHDSINYIQVFKNQGASAGASMSHSHSQMMALPVVPPTVSSRLDGTKDYFEETGKCCLCEAKSKHFVIDESSHFVSVAPFAATYPFEIWIIPKDHSSHFHHLDDVKAVDLGGLLKLMLQKIAKQLNDPPYNYMIHTSPLKVTESQLPYTHWFLQIVPQLSGVGGFEIGTGCYINPVFPEDVAKVMREVSL 350
               SCOP domains --d2q4lb1 B:23-195       Galac           tose-1    -phosphate uridylyltransferase                                                                                              d2q4lb2 B:196-350 Galactose-1-phosphate uridylyltransferase                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee....eeeee..------.....-----------......----....eeeee........eeeee......hhhhh.----------.eee....eeeee............hhhhhhhhhhhhhhhhhhhhh.....eeeeeeeehhhhh......eeeeeee...hhhhhhhhhhhhhhhhhhh.....hhhhheeeeee...eeeeee........eeeee.....hhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeee.........hhhhh..eeeeee.....hhhhhhhh..ee..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2q4l B  21 QSPELRKDPVTNRWVIFSP------TDFKS-----------SCPFCI----ECAPELFRVPDHDPNWKLRVIENLYPALSRNLET----------RTIVGFGFHDVVIESPVHSIQLSDIDPVGIGDILIAYKKRINQIAQHDSINYIQVFKNQGASAGASMSHSHSQMMALPVVPPTVSSRLDGTKDYFEETGKCCLCEAKSKHFVIDESSHFVSVAPFAATYPFEIWIIPKDHSSHFHHLDDVKAVDLGGLLKLMLQKIAKQLNDPPYNYMIHTSPLKVTESQLPYTHWFLQIVPQLSGVGGFEIGTGCYINPVFPEDVAKVMREVSL 350
                                    30        |-     |  50         - |    |  - |      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
                                             39     46  50          62   67   72                              105        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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q4L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Q4L)

(-) Gene Ontology  (13, 13)

Asymmetric 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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 Related Entries

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

UniProtKB/Swiss-Prot
        AGLUP_ARATH | Q9FK51: 1z84 1zwj 2h39 2q4h

(-) Related Entries Specified in the PDB File

1z84 SAME PROTEIN WITH AMP BOUND
1zwj ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET.