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(-) Description

Title :  SUBSTRATE SPECIFICITY AND ASSEMBLY OF CATALYTIC CENTER DERIVED FROM TWO STRUCTURES OF LIGATED URIDYLATE KINASE
 
Authors :  H. -J. Mueller-Dieckmann, G. E. Schulz
Date :  13 Jul 94  (Deposition) - 26 Jan 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.13
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Muller-Dieckmann, G. E. Schulz
Substrate Specificity And Assembly Of The Catalytic Center Derived From Two Structures Of Ligated Uridylate Kinase.
J. Mol. Biol. V. 246 522 1995
PubMed-ID: 7877173  |  Reference-DOI: 10.1006/JMBI.1994.0104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URIDYLATE KINASE
    Chains: A
    EC Number: 2.7.4.-
    Engineered: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:26 , ALA A:27 , GLY A:28 , LYS A:29 , GLY A:30 , THR A:31 , ARG A:138 , ARG A:142 , ARG A:187 , SER A:188 , VAL A:189 , ADP A:206 , HOH A:308 , HOH A:309 , HOH A:326 , HOH A:339 , HOH A:351 , HOH A:361 , HOH A:377BINDING SITE FOR RESIDUE ADP A 205
2AC2SOFTWAREPRO A:25 , LYS A:29 , LEU A:51 , ARG A:52 , ILE A:70 , GLN A:74 , ILE A:75 , VAL A:76 , GLY A:104 , PHE A:105 , ARG A:107 , GLN A:111 , ARG A:142 , ARG A:148 , ARG A:159 , ADP A:205 , HOH A:303 , HOH A:313 , HOH A:359 , HOH A:375 , HOH A:389BINDING SITE FOR RESIDUE ADP A 206

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:130 -A:185

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:105 -Pro A:106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADENYLATE_KINASEPS00113 Adenylate kinase signature.KCY_YEAST100-111  1A:100-111

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YKL024C1YKL024C.1XI:392783-392169615KCY_YEAST1-2042041A:9-204196

(-) 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:196
 aligned with KCY_YEAST | P15700 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:196
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198      
            KCY_YEAST     9 PAFSPDQVSVIFVLGGPGAGKGTQCEKLVKDYSFVHLSAGDLLRAEQGRAGSQYGELIKNCIKEGQIVPQEITLALLRNAISDNVKANKHKFLIDGFPRKMDQAISFERDIVESKFILFFDCPEDIMLERLLERGKTSGRSDDNIESIKKRFNTFKETSMPVIEYFETKSKVVRVRCDRSVEDVYKDVQDAIRDSL 204
               SCOP domains d1ukya_ A: Uridylate kinase                                                                                                                                                                          SCOP domains
               CATH domains 1ukyA00 A:9-204 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee......hhhhhhhhhhh...eee.hhhhhhhhhh.....hhhhhhhhh.......hhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..hhhhhh...eeeee.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------ADENYLATE_KI--------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:9-204 UniProt: 1-204 [INCOMPLETE]                                                                                                                                                   Transcript 1
                 1uky A   9 PAFSPDQVSVIFVLGGPGAGKGTQCEKLVKDYSFVHLSAGDLLRAEQGRAGSQYGELIKNCIKEGQIVPQEITLALLRNAISDNVKANKHKFLIDGFPRKMDQAISFERDIVESKFILFFDCPEDIMLERLLERGKTSGRSDDNIESIKKRFNTFKETSMPVIEYFETKSKVVRVRCDRSVEDVYKDVQDAIRDSL 204
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198
   Legend:   → Mismatch (orange background)
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  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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1UKY)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KCY_YEAST | P15700)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004017    adenylate kinase activity    Catalysis of the reaction: ATP + AMP = 2 ADP.
    GO:0004127    cytidylate kinase activity    Catalysis of the reaction: ATP + (d)CMP = ADP + (d)CDP.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0019205    nucleobase-containing compound kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP or GTP, to a nucleobase, nucleoside, nucleotide or polynucleotide substrate.
    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:0006207    'de novo' pyrimidine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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        KCY_YEAST | P15700: 1ukz

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