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(-) Description

Title :  CRYSTAL STRUCTURE OF UMP KINASE FROM UREAPLASMA PARVUM
 
Authors :  L. Egeblad-Welin, M. Welin, L. Wang, S. Eriksson
Date :  28 Aug 07  (Deposition) - 18 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Umpk, Kinase, Transferase, Uridylate Kinase, Pyrimidine Biosynthesis, Amino Acid Kinase Family (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Egeblad-Welin, M. Welin, L. Wang, S. Eriksson
Structural And Functional Investigations Of Ureaplasma Parvum Ump Kinase - A Potential Antibacterial Drug Target
Febs J. V. 274 6403 2007
PubMed-ID: 18021254  |  Reference-DOI: 10.1111/J.1742-4658.2007.06157.X

(-) Compounds

Molecule 1 - URIDYLATE KINASE
    Chains: A, B, C, D, E, F
    EC Number: 2.7.4.22, 2.7.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-14B
    Organism Scientific: UREAPLASMA PARVUM
    Organism Taxid: 134821
    Synonym: UMP KINASE, UK, URIDINE MONOPHOSPHATE KINASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1PO46Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:11 , GLY A:12 , GLY A:49 , GLY A:50 , GLY A:51 , THR A:138BINDING SITE FOR RESIDUE PO4 A1236
2AC2SOFTWARESER B:11 , GLY B:12 , GLY B:49 , GLY B:50 , GLY B:51 , THR B:138 , HOH B:2027BINDING SITE FOR RESIDUE PO4 B1236
3AC3SOFTWARESER C:11 , GLY C:12 , GLY C:49 , GLY C:50 , GLY C:51 , THR C:138 , HOH C:2027BINDING SITE FOR RESIDUE PO4 C1236
4AC4SOFTWARESER D:11 , GLY D:12 , GLY D:49 , GLY D:50 , GLY D:51 , THR D:138BINDING SITE FOR RESIDUE PO4 D1236
5AC5SOFTWARESER E:11 , GLY E:12 , GLY E:49 , GLY E:50 , GLY E:51 , THR E:138BINDING SITE FOR RESIDUE PO4 E1236
6AC6SOFTWAREGLY F:12 , GLY F:49 , GLY F:50 , GLY F:51 , THR F:138 , HOH F:2017BINDING SITE FOR RESIDUE PO4 F1236

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VA1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VA1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VA1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VA1)

(-) Exons   (0, 0)

(no "Exon" information available for 2VA1)

(-) 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:226
 aligned with PYRH_UREPA | Q9PPX6 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:234
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231    
           PYRH_UREPA     2 RKQRIVIKISGACLKQNDSSIIDFIKINDLAEQIEKISKKYIVSIVLGGGNIWRGSIAKELDMDRNLADNMGMMATIINGLALENALNHLNVNTIVLSAIKCDKLVHESSANNIKKAIEKEQVMIFVAGTGFPYFTTDSCAAIRAAETESSIILMGKNGVDGVYDSDPKINPNAQFYEHITFNMALTQNLKVMDATALALCQENNINLLVFNIDKPNAIVDVLEKKNKYTIVSK 235
               SCOP domains d2va1a_ A: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains 2va1A00 A:2-235  [code=3.40.1160.10, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeehhhhhh.......hhhhhhhhhhhhhhhh...eeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhhh..eeeeee..........--------...eeehhhhhhhh....hhhhhhhhhhh..eeeeee....hhhhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2va1 A   2 RKQRIVIKISGACLKQNDSSIIDFIKINDLAEQIEKISKKYIVSIVLGGGNIWRGSIAKELDMDRNLADNMGMMATIINGLALENALNHLNVNTIVLSAIKCDKLVHESSANNIKKAIEKEQVMIFVAGTGFPYFTTDSCAAIRAAETESSIILMGKNGVDGVYDSD--------FYEHITFNMALTQNLKVMDATALALCQENNINLLVFNIDKPNAIVDVLEKKNKYTIVSK 235
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161      |  -     | 181       191       201       211       221       231    
                                                                                                                                                                                                168      177                                                          


Chain B from PDB  Type:PROTEIN  Length:235
 aligned with PYRH_UREPA | Q9PPX6 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:241
                                  1                                                                                                                                                                                                                                          
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234 
           PYRH_UREPA     - ------MRKQRIVIKISGACLKQNDSSIIDFIKINDLAEQIEKISKKYIVSIVLGGGNIWRGSIAKELDMDRNLADNMGMMATIINGLALENALNHLNVNTIVLSAIKCDKLVHESSANNIKKAIEKEQVMIFVAGTGFPYFTTDSCAAIRAAETESSIILMGKNGVDGVYDSDPKINPNAQFYEHITFNMALTQNLKVMDATALALCQENNINLLVFNIDKPNAIVDVLEKKNKYTIVSK 235
               SCOP domains d2va1b_ B: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains 2va1B00 B:-5-235  [code=3.40.1160.10, no name defined]                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeehhhhhh.......hhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee........------.......eeehhhhhhh.....hhhhhhhhhhh..eeeeee....hhhhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2va1 B  -5 PRGSHMMRKQRIVIKISGACLKQNDSSIIDFIKINDLAEQIEKISKKYIVSIVLGGGNIWRGSIAKELDMDRNLADNMGMMATIINGLALENALNHLNVNTIVLSAIKCDKLVHESSANNIKKAIEKEQVMIFVAGTGFPYFTTDSCAAIRAAETESSIILMGKNGVDGVYD------PNAQFYEHITFNMALTQNLKVMDATALALCQENNINLLVFNIDKPNAIVDVLEKKNKYTIVSK 235
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164 |     174       184       194       204       214       224       234 
                                                                                                                                                                                                     166    173                                                              


Chain C from PDB  Type:PROTEIN  Length:227
 aligned with PYRH_UREPA | Q9PPX6 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:233
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   
           PYRH_UREPA     3 KQRIVIKISGACLKQNDSSIIDFIKINDLAEQIEKISKKYIVSIVLGGGNIWRGSIAKELDMDRNLADNMGMMATIINGLALENALNHLNVNTIVLSAIKCDKLVHESSANNIKKAIEKEQVMIFVAGTGFPYFTTDSCAAIRAAETESSIILMGKNGVDGVYDSDPKINPNAQFYEHITFNMALTQNLKVMDATALALCQENNINLLVFNIDKPNAIVDVLEKKNKYTIVSK 235
               SCOP domains d2va1c_ C: automated matches                                                                                                                                                                                                              SCOP domains
               CATH domains 2va1C00 C:3-235  [code=3.40.1160.10, no name defined]                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhhh.......hhhhhhhhhhhhhhhh...eeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee.....ee...------..ee.eee.hhhhhh.....hhhhhhhhhhh..eeeeee....hhhhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2va1 C   3 KQRIVIKISGACLKQNDSSIIDFIKINDLAEQIEKISKKYIVSIVLGGGNIWRGSIAKELDMDRNLADNMGMMATIINGLALENALNHLNVNTIVLSAIKCDKLVHESSANNIKKAIEKEQVMIFVAGTGFPYFTTDSCAAIRAAETESSIILMGKNGVDGVYDSD------AQFYEHITFNMALTQNLKVMDATALALCQENNINLLVFNIDKPNAIVDVLEKKNKYTIVSK 235
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162     |   -  |    182       192       202       212       222       232   
                                                                                                                                                                                               168    175                                                            


Chain D from PDB  Type:PROTEIN  Length:228
 aligned with PYRH_UREPA | Q9PPX6 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     
           PYRH_UREPA     1 MRKQRIVIKISGACLKQNDSSIIDFIKINDLAEQIEKISKKYIVSIVLGGGNIWRGSIAKELDMDRNLADNMGMMATIINGLALENALNHLNVNTIVLSAIKCDKLVHESSANNIKKAIEKEQVMIFVAGTGFPYFTTDSCAAIRAAETESSIILMGKNGVDGVYDSDPKINPNAQFYEHITFNMALTQNLKVMDATALALCQENNINLLVFNIDKPNAIVDVLEKKNKYTIVSK 235
               SCOP domains d2va1d_ D: automated matches                                                                                                                                                                                                                SCOP domains
               CATH domains 2va1D00 D:1-235  [code=3.40.1160.10, no name defined]                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeehhhhhh.......hhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee.........-------.....eeehhhhhhh.....hhhhhhhhhhh..eeeeee....hhhhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2va1 D   1 MRKQRIVIKISGACLKQNDSSIIDFIKINDLAEQIEKISKKYIVSIVLGGGNIWRGSIAKELDMDRNLADNMGMMATIINGLALENALNHLNVNTIVLSAIKCDKLVHESSANNIKKAIEKEQVMIFVAGTGFPYFTTDSCAAIRAAETESSIILMGKNGVDGVYDS-------AQFYEHITFNMALTQNLKVMDATALALCQENNINLLVFNIDKPNAIVDVLEKKNKYTIVSK 235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      |  -    |  180       190       200       210       220       230     
                                                                                                                                                                                                167     175                                                            


Chain E from PDB  Type:PROTEIN  Length:235
 aligned with PYRH_UREPA | Q9PPX6 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     
           PYRH_UREPA     1 MRKQRIVIKISGACLKQNDSSIIDFIKINDLAEQIEKISKKYIVSIVLGGGNIWRGSIAKELDMDRNLADNMGMMATIINGLALENALNHLNVNTIVLSAIKCDKLVHESSANNIKKAIEKEQVMIFVAGTGFPYFTTDSCAAIRAAETESSIILMGKNGVDGVYDSDPKINPNAQFYEHITFNMALTQNLKVMDATALALCQENNINLLVFNIDKPNAIVDVLEKKNKYTIVSK 235
               SCOP domains d2va1e_ E: automated matches                                                                                                                                                                                                                SCOP domains
               CATH domains 2va1E00 E:1-235  [code=3.40.1160.10, no name defined]                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeehhhhhh.......hhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee.....................eeehhhhhhh.....hhhhhhhhhhh..eeeeee....hhhhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2va1 E   1 MRKQRIVIKISGACLKQNDSSIIDFIKINDLAEQIEKISKKYIVSIVLGGGNIWRGSIAKELDMDRNLADNMGMMATIINGLALENALNHLNVNTIVLSAIKCDKLVHESSANNIKKAIEKEQVMIFVAGTGFPYFTTDSCAAIRAAETESSIILMGKNGVDGVYDSDPKINPNAQFYEHITFNMALTQNLKVMDATALALCQENNINLLVFNIDKPNAIVDVLEKKNKYTIVSK 235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     


Chain F from PDB  Type:PROTEIN  Length:226
 aligned with PYRH_UREPA | Q9PPX6 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:234
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231    
           PYRH_UREPA     2 RKQRIVIKISGACLKQNDSSIIDFIKINDLAEQIEKISKKYIVSIVLGGGNIWRGSIAKELDMDRNLADNMGMMATIINGLALENALNHLNVNTIVLSAIKCDKLVHESSANNIKKAIEKEQVMIFVAGTGFPYFTTDSCAAIRAAETESSIILMGKNGVDGVYDSDPKINPNAQFYEHITFNMALTQNLKVMDATALALCQENNINLLVFNIDKPNAIVDVLEKKNKYTIVSK 235
               SCOP domains d2va1f_ F: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains 2va1F00 F:2-235  [code=3.40.1160.10, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeehhhhhh.......hhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee.........--------....eeehhhhhhh.....hhhhhhhhhhh..eeeeee....hhhhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2va1 F   2 RKQRIVIKISGACLKQNDSSIIDFIKINDLAEQIEKISKKYIVSIVLGGGNIWRGSIAKELDMDRNLADNMGMMATIINGLALENALNHLNVNTIVLSAIKCDKLVHESSANNIKKAIEKEQVMIFVAGTGFPYFTTDSCAAIRAAETESSIILMGKNGVDGVYDS--------QFYEHITFNMALTQNLKVMDATALALCQENNINLLVFNIDKPNAIVDVLEKKNKYTIVSK 235
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161     |   -    |  181       191       201       211       221       231    
                                                                                                                                                                                               167      176
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2VA1)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (PYRH_UREPA | Q9PPX6)
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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