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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN URIDINE-CYTIDINE KINASE 1 IN COMPLEX WITH ADP
 
Authors :  U. Kosinska, P. Stenmark, C. Arrowsmith, H. Berglund, R. Busam, R. Coll A. Edwards, U. B. Ericsson, S. Flodin, A. Flores, S. Graslund, M. Hamma B. M. Hallberg, L. Holmberg Schiavone, M. Hogbom, I. Johansson, T. Ka T. Kotenyova, M. Moche, M. E. P. Nilsson, T. Nyman, D. Ogg, C. Persson, J. Sagemark, M. Sundstrom, J. Uppenberg, M. Uppsten, A. G. Thorsell, S. Van Den Berg, J. Weigelt, M. Welin, P. Nordlund
Date :  13 Mar 07  (Deposition) - 27 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Uck, Kinase, Transferase, Atp-Binding, Nucleoside Kinase, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Kosinska, P. Stenmark, C. Arrowsmith, H. Berglund, R. Busam, R. Collins, A. Edwards, U. B. Ericsson, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, B. M. Hallberg, L. Holmberg Schiavone, M. Hogbom, I. Johansson, T. Karlberg, T. Kotenyova, M. Moche, M. E. P. Nilsson, T. Nyman, D. Ogg, C. Persson, J. Sagemark, M. Sundstrom, J. Uppenberg, M. Uppsten, A. G. Thorsell, S. Van Den Berg, J. Weigelt, M. Welin, P. Nordlund
Structure Of Human Uridine-Cytidine Kinase 1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - URIDINE-CYTIDINE KINASE 1
    Chains: A
    EC Number: 2.7.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-BSA4
    Expression System Taxid: 562
    Fragment: RESIDUES 22-243
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: UCK 1, URIDINE MONOPHOSPHOKINASE 1, CYTIDINE MONOPHOSPHOKINASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:32 , ALA A:33 , SER A:34 , GLY A:35 , LYS A:36 , SER A:37 , THR A:38 , GLU A:138 , ARG A:168 , ARG A:172 , VAL A:214 , ASP A:215BINDING SITE FOR RESIDUE ADP A1236

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:22 -Pro A:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (7, 7)

Asymmetric Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003722151aENSE00001945595chr9:134406655-134406454202UCK1_HUMAN1-36361A:22-3615
1.2bENST000003722152bENSE00001729279chr9:134406032-134405873160UCK1_HUMAN37-90541A:37-9054
1.3aENST000003722153aENSE00000896255chr9:134404971-13440487597UCK1_HUMAN90-122331A:90-12233
1.4aENST000003722154aENSE00000896253chr9:134404657-134404515143UCK1_HUMAN122-170491A:122-17049
1.4dENST000003722154dENSE00000896250chr9:134404425-13440433195UCK1_HUMAN170-201321A:170-201 (gaps)32
1.6cENST000003722156cENSE00001783980chr9:134401364-13440131649UCK1_HUMAN202-218171A:202-21817
1.7cENST000003722157cENSE00001933761chr9:134400608-1343991881421UCK1_HUMAN218-277601A:218-23518

(-) 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:211
 aligned with UCK1_HUMAN | Q9HA47 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:214
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231    
           UCK1_HUMAN    22 RPFLIGVSGGTASGKSTVCEKIMELLGQNEVEQRQRKVVILSQDRFYKVLTAEQKAKALKGQYNFDHPDAFDNDLMHRTLKNIVEGKTVEVPTYDFVTHSRLPETTVVYPADVVLFEGILVFYSQEIRDMFHLRLFVDTDSDVRLSRRVLRDVRRGRDLEQILTQYTTFVKPAFEEFCLPTKKYADVIIPRGVDNMVAINLIVQHIQDILNGDI 235
               SCOP domains d2uvqa_ A: automated matches                                                                                                                                                                                           SCOP domains
               CATH domains 2uvqA00 A:22-235 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                  CATH domains
               Pfam domains ---PRK-2uvqA01 A:25-219                                                                                                                                                                               ---------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhhhhh......eeeee.hhh....hhhhhhhhhh......hhhh.hhhhhhhhhhhhhh...eee.eee....eee...eee....eeeee......hhhhhh...eeeeee.hhhhhhhhhhhhh..---hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a      Exon 1.2b  PDB: A:37-90 UniProt: 37-90                -------------------------------Exon 1.4a  PDB: A:122-170 UniProt: 122-170       -------------------------------Exon 1.6c        ----------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------Exon 1.3a  PDB: A:90-122         -----------------------------------------------Exon 1.4d  PDB: A:170-201 (gaps)----------------Exon 1.7c          Transcript 1 (2)
                 2uvq A  22 RPFLIGVSGGTASGKSTVCEKIMELLGQNEVEQRQRKVVILSQDRFYKVLTAEQKAKALKGQYNFDHPDAFDNDLMHRTLKNIVEGKTVEVPTYDFVTHSRLPETTVVYPADVVLFEGILVFYSQEIRDMFHLRLFVDTDSDVRLSRRVLRDVR---DLEQILTQYTTFVKPAFEEFCLPTKKYADVIIPRGVDNMVAINLIVQHIQDILNGDI 235
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171   |   181       191       201       211       221       231    
                                                                                                                                                                                   175 179
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (UCK1_HUMAN | Q9HA47)
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: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: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

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        UCK1_HUMAN | Q9HA47: 2jeo

(-) Related Entries Specified in the PDB File

2jeo CRYSTAL STRUCTURE OF HUMAN URIDINE-CYTIDINE KINASE 1