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(-) Description

Title :  UNIQUE GTP-BINDING POCKET AND ALLOSTERY OF UMP KINASE FROM A GRAM-NEGATIVE PHYTOPATHOGEN BACTERIUM
 
Authors :  J. -L. Tu, K. -H. Chin, A. H. -J. Wang, S. -H. Chou
Date :  18 Sep 08  (Deposition) - 23 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.34
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (1x)
Biol. Unit 2:  A,C  (1x)
Biol. Unit 3:  B,D  (1x)
Biol. Unit 4:  E,F  (1x)
Keywords :  Xanthomonas Campestris, Umpk Crystal Structure, Unique Gtp Binding Site, Allosteric Regulation, Atp-Binding, Kinase, Nucleotide- Binding, Pyrimidine Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. -L. Tu, K. -H. Chin, A. H. -J. Wang, S. -H. Chou
Unique Gtp-Binding Pocket And Allostery Of Uridylate Kinase From A Gram-Negative Phytopathogenic Bacterium
J. Mol. Biol. V. 385 1113 2009
PubMed-ID: 19059268  |  Reference-DOI: 10.1016/J.JMB.2008.11.030

(-) Compounds

Molecule 1 - URIDYLATE KINASE
    Chains: A, B, C, D, E, F
    EC Number: 2.7.4.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PYRH, XCC1371
    Organism Scientific: XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS
    Organism Taxid: 340
    Strain: XC17
    Synonym: UK, URIDINE MONOPHOSPHATE KINASE, UMP KINASE, UMPK

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABCDEF
Biological Unit 2 (1x): A C   
Biological Unit 3 (1x):  B D  
Biological Unit 4 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3EK6)

(-) Sites  (0, 0)

(no "Site" information available for 3EK6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EK6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EK6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EK6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EK6)

(-) Exons   (0, 0)

(no "Exon" information available for 3EK6)

(-) 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:243
 aligned with PYRH_XANCP | P59009 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:243
                               1                                                                                                                                                                                                                                               
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237   
           PYRH_XANCP     - ---MSELSYRRILLKLSGEALMGDGDYGIDPKVINRLAHEVIEAQQAGAQVALVIGGGNIFRGAGLAASGMDRVTGDHMGMLATVINALAMQDALEKLGAKVRVMSAIKINDVCEDFIRRRAIRHLEKGRIAIFAAGTGNPFFTTDSGAALRAIEIGADLLLKATKVDGVYDKDPKKHSDAVRYDSLTYDEVIMQGLEVMDTAAFALARDSDLPLRIFGMSEPGVLLRILHGAQIGTLVQGRS 240
               SCOP domains d3ek6a_ A: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains 3ek6A00 A:-2-240  [code=3.40.1160.10, no name defined]                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...eeeeeehhhhhh.......hhhhhhhhhhhhhhhhhh..eeeeee................hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhhh..eeeee.........hhhhh.......eehhhhhhhhh....hhhhhhhhhhh...eeee.....hhhhhhhh.....eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ek6 A  -2 SNAMSELSYRRILLKLSGEALMGDGDYGIDPKVINRLAHEVIEAQQAGAQVALVIGGGNIFRGAGLAASGMDRVTGDHMGMLATVINALAMQDALEKLGAKVRVMSAIKINDVCEDFIRRRAIRHLEKGRIAIFAAGTGNPFFTTDSGAALRAIEIGADLLLKATKVDGVYDKDPKKHSDAVRYDSLTYDEVIMQGLEVMDTAAFALARDSDLPLRIFGMSEPGVLLRILHGAQIGTLVQGRS 240
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237   


Chain B from PDB  Type:PROTEIN  Length:240
 aligned with PYRH_XANCP | P59009 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
           PYRH_XANCP     1 MSELSYRRILLKLSGEALMGDGDYGIDPKVINRLAHEVIEAQQAGAQVALVIGGGNIFRGAGLAASGMDRVTGDHMGMLATVINALAMQDALEKLGAKVRVMSAIKINDVCEDFIRRRAIRHLEKGRIAIFAAGTGNPFFTTDSGAALRAIEIGADLLLKATKVDGVYDKDPKKHSDAVRYDSLTYDEVIMQGLEVMDTAAFALARDSDLPLRIFGMSEPGVLLRILHGAQIGTLVQGRS 240
               SCOP domains d3ek6b_ B: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains 3ek6B00 B:1-240  [code=3.40.1160.10, no name defined]                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhh..eeeeee................hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhhh..eeeee.....................eehhhhhhhh.....hhhhhhhhhhh...eeee.....hhhhhhhh.....eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ek6 B   1 MSELSYRRILLKLSGEALMGDGDYGIDPKVINRLAHEVIEAQQAGAQVALVIGGGNIFRGAGLAASGMDRVTGDHMGMLATVINALAMQDALEKLGAKVRVMSAIKINDVCEDFIRRRAIRHLEKGRIAIFAAGTGNPFFTTDSGAALRAIEIGADLLLKATKVDGVYDKDPKKHSDAVRYDSLTYDEVIMQGLEVMDTAAFALARDSDLPLRIFGMSEPGVLLRILHGAQIGTLVQGRS 240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240


Chain C from PDB  Type:PROTEIN  Length:238
 aligned with PYRH_XANCP | P59009 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:238
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232        
           PYRH_XANCP     3 ELSYRRILLKLSGEALMGDGDYGIDPKVINRLAHEVIEAQQAGAQVALVIGGGNIFRGAGLAASGMDRVTGDHMGMLATVINALAMQDALEKLGAKVRVMSAIKINDVCEDFIRRRAIRHLEKGRIAIFAAGTGNPFFTTDSGAALRAIEIGADLLLKATKVDGVYDKDPKKHSDAVRYDSLTYDEVIMQGLEVMDTAAFALARDSDLPLRIFGMSEPGVLLRILHGAQIGTLVQGRS 240
               SCOP domains d3ek6c_ C: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 3ek6C00 C:3-240  [code=3.40.1160.10, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeehhhhhh.......hhhhhhhhhhhhhhhhhh..eeeeee................hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeee.....ee...........ee.eehhhhhhhh.....hhhhhhhhhhh...eeee.....hhhhhhhh.....eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ek6 C   3 ELSYRRILLKLSGEALMGDGDYGIDPKVINRLAHEVIEAQQAGAQVALVIGGGNIFRGAGLAASGMDRVTGDHMGMLATVINALAMQDALEKLGAKVRVMSAIKINDVCEDFIRRRAIRHLEKGRIAIFAAGTGNPFFTTDSGAALRAIEIGADLLLKATKVDGVYDKDPKKHSDAVRYDSLTYDEVIMQGLEVMDTAAFALARDSDLPLRIFGMSEPGVLLRILHGAQIGTLVQGRS 240
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232        


Chain D from PDB  Type:PROTEIN  Length:240
 aligned with PYRH_XANCP | P59009 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
           PYRH_XANCP     1 MSELSYRRILLKLSGEALMGDGDYGIDPKVINRLAHEVIEAQQAGAQVALVIGGGNIFRGAGLAASGMDRVTGDHMGMLATVINALAMQDALEKLGAKVRVMSAIKINDVCEDFIRRRAIRHLEKGRIAIFAAGTGNPFFTTDSGAALRAIEIGADLLLKATKVDGVYDKDPKKHSDAVRYDSLTYDEVIMQGLEVMDTAAFALARDSDLPLRIFGMSEPGVLLRILHGAQIGTLVQGRS 240
               SCOP domains d3ek6d_ D: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains 3ek6D00 D:1-240  [code=3.40.1160.10, no name defined]                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhh..eeeeee................hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeee.....................eehhhhhhhh.....hhhhhhhhhhh...eeee.....hhhhhhhh.....eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ek6 D   1 MSELSYRRILLKLSGEALMGDGDYGIDPKVINRLAHEVIEAQQAGAQVALVIGGGNIFRGAGLAASGMDRVTGDHMGMLATVINALAMQDALEKLGAKVRVMSAIKINDVCEDFIRRRAIRHLEKGRIAIFAAGTGNPFFTTDSGAALRAIEIGADLLLKATKVDGVYDKDPKKHSDAVRYDSLTYDEVIMQGLEVMDTAAFALARDSDLPLRIFGMSEPGVLLRILHGAQIGTLVQGRS 240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240


Chain E from PDB  Type:PROTEIN  Length:238
 aligned with PYRH_XANCP | P59009 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:238
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232        
           PYRH_XANCP     3 ELSYRRILLKLSGEALMGDGDYGIDPKVINRLAHEVIEAQQAGAQVALVIGGGNIFRGAGLAASGMDRVTGDHMGMLATVINALAMQDALEKLGAKVRVMSAIKINDVCEDFIRRRAIRHLEKGRIAIFAAGTGNPFFTTDSGAALRAIEIGADLLLKATKVDGVYDKDPKKHSDAVRYDSLTYDEVIMQGLEVMDTAAFALARDSDLPLRIFGMSEPGVLLRILHGAQIGTLVQGRS 240
               SCOP domains d3ek6e_ E: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 3ek6E00 E:3-240  [code=3.40.1160.10, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhh..eeeeee......hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeee.....................eehhhhhhhh.....hhhhhhhhhhh...eeee.....hhhhhhhh.....eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ek6 E   3 ELSYRRILLKLSGEALMGDGDYGIDPKVINRLAHEVIEAQQAGAQVALVIGGGNIFRGAGLAASGMDRVTGDHMGMLATVINALAMQDALEKLGAKVRVMSAIKINDVCEDFIRRRAIRHLEKGRIAIFAAGTGNPFFTTDSGAALRAIEIGADLLLKATKVDGVYDKDPKKHSDAVRYDSLTYDEVIMQGLEVMDTAAFALARDSDLPLRIFGMSEPGVLLRILHGAQIGTLVQGRS 240
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232        


Chain F from PDB  Type:PROTEIN  Length:238
 aligned with PYRH_XANCP | P59009 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:238
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232        
           PYRH_XANCP     3 ELSYRRILLKLSGEALMGDGDYGIDPKVINRLAHEVIEAQQAGAQVALVIGGGNIFRGAGLAASGMDRVTGDHMGMLATVINALAMQDALEKLGAKVRVMSAIKINDVCEDFIRRRAIRHLEKGRIAIFAAGTGNPFFTTDSGAALRAIEIGADLLLKATKVDGVYDKDPKKHSDAVRYDSLTYDEVIMQGLEVMDTAAFALARDSDLPLRIFGMSEPGVLLRILHGAQIGTLVQGRS 240
               SCOP domains d3ek6f_ F: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 3ek6F00 F:3-240  [code=3.40.1160.10, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeehhhhhh.......hhhhhhhhhhhhhhhhhh..eeeeee......hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........ee.hhhhhhhhhh...eeeee........hhhhhhhhhhhhh...eeeee.....................eehhhhhhhhh....hhhhhhhhhhh...eeee.....hhhhhhhhh....eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ek6 F   3 ELSYRRILLKLSGEALMGDGDYGIDPKVINRLAHEVIEAQQAGAQVALVIGGGNIFRGAGLAASGMDRVTGDHMGMLATVINALAMQDALEKLGAKVRVMSAIKINDVCEDFIRRRAIRHLEKGRIAIFAAGTGNPFFTTDSGAALRAIEIGADLLLKATKVDGVYDKDPKKHSDAVRYDSLTYDEVIMQGLEVMDTAAFALARDSDLPLRIFGMSEPGVLLRILHGAQIGTLVQGRS 240
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
   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, 6)

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

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EK6)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (PYRH_XANCP | P59009)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0033862    UMP kinase activity    Catalysis of the reaction: ATP + UMP = ADP + UDP.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0009041    uridylate kinase activity    Catalysis of the reaction: ATP + (d)UMP = ADP + (d)UDP.
biological process
    GO:0044210    'de novo' CTP biosynthetic process    The chemical reactions and pathways resulting in the formation of cytidine 5'-triphosphate (CTP) from simpler components.
    GO:0046939    nucleotide phosphorylation    The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  3ek6
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  PYRH_XANCP | P59009
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  2.7.4.22
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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRH_XANCP | P59009: 3ek5

(-) Related Entries Specified in the PDB File

3ek5 THE SAME PROTEIN COMPLEXD WITH GTP