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(-) Description

Title :  THE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH UMP
 
Authors :  P. Briozzo, C. Evrin, P. Meyer, L. Assairi, N. Joly, O. Barzu, A. M. Gilles
Date :  23 Mar 05  (Deposition) - 25 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Transferase, Nucleoside Monophosphate Kinase, Pyrimidine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Briozzo, C. Evrin, P. Meyer, L. Assairi, N. Joly, O. Barzu, A. M. Gilles
Structure Of Escherichia Coli Ump Kinase Differs From That Of Other Nucleoside Monophosphate Kinases And Sheds New Light On Enzyme Regulation.
J. Biol. Chem. V. 280 25533 2005
PubMed-ID: 15857829  |  Reference-DOI: 10.1074/JBC.M501849200

(-) Compounds

Molecule 1 - URIDYLATE KINASE
    ChainsA, B
    EC Number2.7.4.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12
    SynonymUMP KINASE, UK, URIDINE MONOPHOSPHATE KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (3x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2U5P2Ligand/IonURIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (2, 27)
No.NameCountTypeFull Name
1GOL21Ligand/IonGLYCEROL
2U5P6Ligand/IonURIDINE-5'-MONOPHOSPHATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:56 , GLY A:57 , GLY A:58 , ARG A:62 , GLY A:63 , ASP A:77 , GLY A:80 , MET A:81 , THR A:138 , ASN A:140 , PRO A:141 , PHE A:143 , THR A:144 , THR A:145 , HOH A:2015 , HOH A:2042BINDING SITE FOR RESIDUE U5P A1242
2AC2SOFTWAREGLY B:56 , GLY B:57 , GLY B:58 , ARG B:62 , GLY B:63 , ASP B:77 , GLY B:80 , MET B:81 , THR B:84 , THR B:138 , ASN B:140 , PRO B:141 , PHE B:143 , THR B:144 , THR B:145 , HOH B:2023BINDING SITE FOR RESIDUE U5P B1242
3AC3SOFTWAREGLN A:39 , LYS A:42 , GOL A:1244 , HOH A:2043 , GLN B:39 , GLU B:46 , GOL B:1244BINDING SITE FOR RESIDUE GOL A1243
4AC4SOFTWAREGLN A:39 , GLU A:46 , GOL A:1243 , GLN B:39 , LYS B:42BINDING SITE FOR RESIDUE GOL A1244
5AC5SOFTWAREVAL A:192 , LEU A:193 , GLU A:196 , LEU A:197 , VAL A:199 , MET A:200BINDING SITE FOR RESIDUE GOL A1245
6AC6SOFTWARETYR A:99 , VAL A:100 , ASN A:101 , ARG A:127BINDING SITE FOR RESIDUE GOL A1246
7AC7SOFTWAREHIS A:211 , ARG B:73BINDING SITE FOR RESIDUE GOL B1243
8AC8SOFTWARELYS A:195 , GOL A:1243 , GLN B:39 , GLU B:43 , ARG B:227BINDING SITE FOR RESIDUE GOL B1244
9AC9SOFTWARELYS B:10 , GLN B:50 , ARG B:127 , ASN B:129 , HOH B:2004 , HOH B:2052BINDING SITE FOR RESIDUE GOL B1245

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PYRH_ECOLI_001 *R62HPYRH_ECOLI  ---  ---A/BR62H
2UniProtVAR_PYRH_ECOLI_002 *D201NPYRH_ECOLI  ---  ---A/BD201N
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PYRH_ECOLI_001 *R62HPYRH_ECOLI  ---  ---A/BR62H
2UniProtVAR_PYRH_ECOLI_002 *D201NPYRH_ECOLI  ---  ---A/BD201N
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BNE)

(-) 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:234
 aligned with PYRH_ECO57 | P0A7F1 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:237
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       
           PYRH_ECO57     5 AKPVYKRILLKLSGEALQGTEGFGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEADVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE 241
               SCOP domains d2bnea_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2bneA00 A:5-241  [code=3.40.1160.10, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee..........---.......eeehhhhhhh.....hhhhhhhhhhh...eeeee....hhhhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------N---------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bne A   5 AKPVYKRILLKLSGEALQGTEGFGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEANVVLKATKVDGVFTADP---PTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE 241
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174|   |  184       194       204       214       224       234       
                                                                                                                                                                                                    175 179                                                              

Chain A from PDB  Type:PROTEIN  Length:234
 aligned with PYRH_ECOL6 | P0A7F0 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:237
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       
           PYRH_ECOL6     5 AKPVYKRILLKLSGEALQGTEGFGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEADVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE 241
               SCOP domains d2bnea_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2bneA00 A:5-241  [code=3.40.1160.10, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee..........---.......eeehhhhhhh.....hhhhhhhhhhh...eeeee....hhhhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------N---------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bne A   5 AKPVYKRILLKLSGEALQGTEGFGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEANVVLKATKVDGVFTADP---PTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE 241
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174|   |  184       194       204       214       224       234       
                                                                                                                                                                                                    175 179                                                              

Chain A from PDB  Type:PROTEIN  Length:234
 aligned with PYRH_ECOLI | P0A7E9 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:237
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       
           PYRH_ECOLI     5 AKPVYKRILLKLSGEALQGTEGFGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEADVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE 241
               SCOP domains d2bnea_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2bneA00 A:5-241  [code=3.40.1160.10, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee..........---.......eeehhhhhhh.....hhhhhhhhhhh...eeeee....hhhhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------N---------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bne A   5 AKPVYKRILLKLSGEALQGTEGFGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEANVVLKATKVDGVFTADP---PTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE 241
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174|   |  184       194       204       214       224       234       
                                                                                                                                                                                                    175 179                                                              

Chain A from PDB  Type:PROTEIN  Length:234
 aligned with PYRH_SHIFL | P0A7F2 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:237
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       
           PYRH_SHIFL     5 AKPVYKRILLKLSGEALQGTEGFGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEADVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE 241
               SCOP domains d2bnea_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2bneA00 A:5-241  [code=3.40.1160.10, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee..........---.......eeehhhhhhh.....hhhhhhhhhhh...eeeee....hhhhhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------N---------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bne A   5 AKPVYKRILLKLSGEALQGTEGFGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEANVVLKATKVDGVFTADP---PTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE 241
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174|   |  184       194       204       214       224       234       
                                                                                                                                                                                                    175 179                                                              

Chain B from PDB  Type:PROTEIN  Length:238
 aligned with PYRH_ECO57 | P0A7F1 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:239
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232         
           PYRH_ECO57     3 TNAKPVYKRILLKLSGEALQGTEGFGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEADVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE 241
               SCOP domains d2bneb_ B: automated ma tches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2bneB00 B:3-241  [code= 3.40.1160.10, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.hhhhhh..-...hhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee....................eee.hhhhhh.....hhhhhhhhhhh...eeeee....hhhhhhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------N---------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bne B   3 TNAKPVYKRILLKLSGEALQGTE-FGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEANVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE 241
                                    12        22  | |   32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232         
                                                 25 |                                                                                                                                                                                                                      
                                                   27                                                                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:238
 aligned with PYRH_ECOL6 | P0A7F0 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:239
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232         
           PYRH_ECOL6     3 TNAKPVYKRILLKLSGEALQGTEGFGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEADVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE 241
               SCOP domains d2bneb_ B: automated ma tches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2bneB00 B:3-241  [code= 3.40.1160.10, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.hhhhhh..-...hhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee....................eee.hhhhhh.....hhhhhhhhhhh...eeeee....hhhhhhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------N---------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bne B   3 TNAKPVYKRILLKLSGEALQGTE-FGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEANVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE 241
                                    12        22  | |   32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232         
                                                 25 |                                                                                                                                                                                                                      
                                                   27                                                                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:238
 aligned with PYRH_ECOLI | P0A7E9 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:239
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232         
           PYRH_ECOLI     3 TNAKPVYKRILLKLSGEALQGTEGFGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEADVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE 241
               SCOP domains d2bneb_ B: automated ma tches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2bneB00 B:3-241  [code= 3.40.1160.10, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.hhhhhh..-...hhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee....................eee.hhhhhh.....hhhhhhhhhhh...eeeee....hhhhhhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------N---------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bne B   3 TNAKPVYKRILLKLSGEALQGTE-FGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEANVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE 241
                                    12        22  | |   32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232         
                                                 25 |                                                                                                                                                                                                                      
                                                   27                                                                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:238
 aligned with PYRH_SHIFL | P0A7F2 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:239
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232         
           PYRH_SHIFL     3 TNAKPVYKRILLKLSGEALQGTEGFGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEADVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE 241
               SCOP domains d2bneb_ B: automated ma tches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2bneB00 B:3-241  [code= 3.40.1160.10, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.hhhhhh..-...hhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........ee.hhhhhhhhhhh..eeeee........hhhhhhhhhhhhh...eeeeee....................eee.hhhhhh.....hhhhhhhhhhh...eeeee....hhhhhhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------N---------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bne B   3 TNAKPVYKRILLKLSGEALQGTE-FGIDASILDRMAQEIKELVELGIQVGVVIGGGNLFRGAGLAKAGMNRVVGDHMGMLATVMNGLAMRDALHRAYVNARLMSAIPLNGVCDSYSWAEAISLLRNNRVVILSAGTGNPFFTTDSAACLRGIEIEANVVLKATKVDGVFTADPAKDPTATMYEQLTYSEVLEKELKVMDLAAFTLARDHKLPIRVFNMNKPGALRRVVMGEKEGTLITE 241
                                    12        22  | |   32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232         
                                                 25 |                                                                                                                                                                                                                      
                                                   27                                                                                                                                                                                                                      

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 54)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PYRH_ECOLI | P0A7E9)
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: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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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: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: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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain A,B   (PYRH_ECO57 | P0A7F1)
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: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: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: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: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.

Chain A,B   (PYRH_ECOL6 | P0A7F0)
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: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: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: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: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.

Chain A,B   (PYRH_SHIFL | P0A7F2)
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: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: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: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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRH_ECO57 | P0A7F12bnd 2bnf
        PYRH_ECOL6 | P0A7F02bnd 2bnf
        PYRH_ECOLI | P0A7E92bnd 2bnf 2v4y
        PYRH_SHIFL | P0A7F22bnd 2bnf

(-) Related Entries Specified in the PDB File

2bnd THE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH UDP
2bnf THE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH UTP