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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN URIDINE-CYTIDINE KINASE 2 COMPLEXED WITH A SUBSTRATE, CYTIDINE
 
Authors :  N. N. Suzuki, K. Koizumi, M. Fukushima, A. Matsuda, F. Inagaki
Date :  16 May 03  (Deposition) - 04 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha/Beta Mononucleotide-Binding Hold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. N. Suzuki, K. Koizumi, M. Fukushima, A. Matsuda, F. Inagaki
Structural Basis For The Specificity, Catalysis, And Regulation Of Human Uridine-Cytidine Kinase
Structure V. 12 751 2004
PubMed-ID: 15130468  |  Reference-DOI: 10.1016/J.STR.2004.02.038
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URIDINE-CYTIDINE KINASE 2
    ChainsA, B
    EC Number2.7.1.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-6P
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-250
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymURIDINE-CYTIDINE KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2CTN2Ligand/Ion4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CTN1Ligand/Ion4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CTN1Ligand/Ion4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:62 , TYR A:65 , PHE A:83 , ASP A:84 , TYR A:112 , HIS A:117 , ARG A:166 , ARG A:174 , ARG A:176 , GLN A:184 , HOH A:303 , HOH A:322BINDING SITE FOR RESIDUE CTN A 301
2AC2SOFTWAREASP B:62 , TYR B:65 , PHE B:83 , ASP B:84 , TYR B:112 , PHE B:114 , HIS B:117 , ARG B:166 , ARG B:174 , ARG B:176 , GLN B:184BINDING SITE FOR RESIDUE CTN B 1301
3AC3SOFTWAREALA A:30 , SER A:31 , GLY A:32 , LYS A:33 , SER A:34 , SER A:35 , ARG A:169 , HOH A:322BINDING SITE FOR RESIDUE CIT A 302
4AC4SOFTWAREALA B:30 , SER B:31 , GLY B:32 , LYS B:33 , SER B:34 , SER B:35 , ARG B:169BINDING SITE FOR RESIDUE CIT B 1302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UEJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UEJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UEJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UEJ)

(-) Exons   (7, 14)

Asymmetric Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003678791aENSE00001445845chr1:165796768-165797169402UCK2_HUMAN1-33332A:19-33
B:18-33
15
16
1.2ENST000003678792ENSE00001656332chr1:165859441-165859600160UCK2_HUMAN34-87542A:34-87 (gaps)
B:34-87 (gaps)
54
54
1.3ENST000003678793ENSE00000958515chr1:165860463-16586055997UCK2_HUMAN87-119332A:87-119
B:87-119
33
33
1.6cENST000003678796cENSE00001157917chr1:165865427-165865569143UCK2_HUMAN119-167492A:119-167
B:119-167
49
49
1.8bENST000003678798bENSE00001600798chr1:165872419-16587251698UCK2_HUMAN167-199332A:167-199
B:167-199
33
33
1.10ENST0000036787910ENSE00001756761chr1:165875158-16587520649UCK2_HUMAN200-216172A:200-216
B:200-216
17
17
1.11gENST0000036787911gENSE00001955918chr1:165876921-165877346426UCK2_HUMAN216-261462A:216-229
B:216-230
14
15

(-) 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:205
 aligned with UCK2_HUMAN | Q9BZX2 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:211
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228 
           UCK2_HUMAN    19 EPFLIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQDSFYRVLTSEQKAKALKGQFNFDHPDAFDNELILKTLKEITEGKTVQIPVYDFVSHSRKEETVTVYPADVVLFEGILAFYSQEVRDLFQMKLFVDTDADTRLSRRVLRDISERGRDLEQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDIL 229
               SCOP domains d1ueja_ A: Uridine-cytidine       kinase 2                                                                                                                                                                          SCOP domains
               CATH domains 1uejA00 A:19-229 P-loop cont      aining nucleotide triphosphate hydrolases                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhh------...eeeee.hhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...eeeeeee....eeeeeeeee....eeeeee.....hhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a      Exon 1.2  PDB: A:34-87 (gaps) UniProt: 34-87          -------------------------------Exon 1.6c  PDB: A:119-167 UniProt: 119-167       --------------------------------Exon 1.10        ------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------Exon 1.3  PDB: A:87-119          -----------------------------------------------Exon 1.8b  PDB: A:167-199        ----------------Exon 1.11g     Transcript 1 (2)
                 1uej A  19 EPFLIGVSGGTASGKSSVCAKIVQLLGQ------QKQVVILSQDSFYRVLTSEQKAKALKGQFNFDHPDAFDNELILKTLKEITEGKTVQIPVYDFVSHSRKEETVTVYPADVVLFEGILAFYSQEVRDLFQMKLFVDTDADTRLSRRVLRDISERGRDLEQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDIL 229
                                    28        38       | -    |   58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228 
                                                      46     53                                                                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:207
 aligned with UCK2_HUMAN | Q9BZX2 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:213
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227   
           UCK2_HUMAN    18 GEPFLIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQDSFYRVLTSEQKAKALKGQFNFDHPDAFDNELILKTLKEITEGKTVQIPVYDFVSHSRKEETVTVYPADVVLFEGILAFYSQEVRDLFQMKLFVDTDADTRLSRRVLRDISERGRDLEQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDILN 230
               SCOP domains d1uejb_ B: Uridine-cytidine k      inase 2                                                                                                                                                                            SCOP domains
               CATH domains 1uejB00 B:18-230 P-loop conta      ining nucleotide triphosphate hydrolases                                                                                                                                           CATH domains
           Pfam domains (1) ----PRK-1uejB01 B:22-217                                                                                                                                                                                ------------- Pfam domains (1)
           Pfam domains (2) ----PRK-1uejB02 B:22-217                                                                                                                                                                                ------------- Pfam domains (2)
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhh------...eeeee.hhhh...hhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...eeeeeee....eeeeeeeee....eeeeee.....hhhhhh...eeeeee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a       Exon 1.2  PDB: B:34-87 (gaps) UniProt: 34-87          -------------------------------Exon 1.6c  PDB: B:119-167 UniProt: 119-167       --------------------------------Exon 1.10        -------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------Exon 1.3  PDB: B:87-119          -----------------------------------------------Exon 1.8b  PDB: B:167-199        ----------------Exon 1.11g      Transcript 1 (2)
                 1uej B  18 GEPFLIGVSGGTASGKSSVCAKIVQLLGQ------QKQVVILSQDSFYRVLTSEQKAKALKGQFNFDHPDAFDNELILKTLKEITEGKTVQIPVYDFVSHSRKEETVTVYPADVVLFEGILAFYSQEVRDLFQMKLFVDTDADTRLSRRVLRDISERGRDLEQILSQYITFVKPAFEEFCLPTKKYADVIIPRGADNLVAINLIVQHIQDILN 230
                                    27        37        |-     |  57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227   
                                                       46     53                                                                                                                                                                                 

   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  (1, 2)

Asymmetric Unit
(-)
Family: PRK (16)
1aPRK-1uejB01B:22-217
1bPRK-1uejB02B:22-217

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (UCK2_HUMAN | Q9BZX2)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0019206    nucleoside kinase activity    Catalysis of the reaction: ATP + nucleoside = ADP + nucleoside monophosphate.
    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:0004849    uridine kinase activity    Catalysis of the reaction: ATP + uridine = ADP + UMP.
biological process
    GO:0006238    CMP salvage    Any process that generates CMP, cytidine monophosphate, from derivatives of it without de novo synthesis.
    GO:0044211    CTP salvage    Any process which produces cytidine 5'-triphosphate (CTP) from derivatives of it, without de novo synthesis.
    GO:0044206    UMP salvage    Any process which produces UMP, uridine monophosphate, from derivatives of it (e.g. cytidine, uridine, cytosine) without de novo synthesis.
    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: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:0006206    pyrimidine nucleobase metabolic process    The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
    GO:0043097    pyrimidine nucleoside salvage    Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UCK2_HUMAN | Q9BZX21udw 1uei 1ufq 1uj2 1xrj

(-) Related Entries Specified in the PDB File

1udw THE SAME PROTEIN COMPLEXED WITH CTP.
1uei THE SAME PROTEIN COMPLEXED WITH UTP.