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(-) Description

Title :  PH INFLUENCES FLUORIDE COORDINATION NUMBER OF THE ALFX PHOSPHORYL TRANSFER TRANSITION STATE ANALOG IN UMP/CMP KINASE
 
Authors :  I. Schlichting, J. Reinstein
Date :  07 Apr 99  (Deposition) - 16 Aug 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Nucleoside Monophosphate Kinase, Nmp Kinase, Phosphoryl Transfer, Transition State Analog Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Schlichting, J. Reinstein
Ph Influences Fluoride Coordination Number Of The Alfx Phosphoryl Transfer Transition State Analog.
Nat. Struct. Biol. V. 6 721 1999
PubMed-ID: 10426946  |  Reference-DOI: 10.1038/11485
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (URIDYLMONOPHOSPHATE/CYTIDYLMONOPHOSPHATE KINASE)
    Chains: A
    EC Number: 2.7.4.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: KCY_DICDI
    Expression System Plasmid: PIMS5-CDUK-1
    Expression System Taxid: 562
    Gene: KCY_DICDI
    Organism Scientific: DICTYOSTELIUM DISCOIDEUM
    Organism Taxid: 44689
    Strain: AX2-214
    Synonym: UMP/CMP KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ALF1Ligand/IonTETRAFLUOROALUMINATE ION
3C5P1Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
4MG1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:15 , GLY A:16 , LYS A:19 , ARG A:93 , ARG A:131 , ARG A:137 , ARG A:148 , ADP A:195 , C5P A:196 , HOH A:198 , MG A:500BINDING SITE FOR RESIDUE ALF A 499
2AC2SOFTWAREADP A:195 , HOH A:198 , HOH A:215 , HOH A:220 , HOH A:227 , ALF A:499BINDING SITE FOR RESIDUE MG A 500
3AC3SOFTWAREGLY A:16 , SER A:17 , GLY A:18 , LYS A:19 , GLY A:20 , THR A:21 , ARG A:127 , ARG A:131 , ARG A:176 , VAL A:178 , HOH A:216 , HOH A:220 , HOH A:232 , HOH A:239 , ALF A:499 , MG A:500 , HOH A:606 , HOH A:778 , HOH A:891BINDING SITE FOR RESIDUE ADP A 195
4AC4SOFTWAREGLY A:38 , LEU A:41 , ARG A:42 , ILE A:59 , GLU A:63 , ILE A:64 , VAL A:65 , GLY A:90 , PHE A:91 , ARG A:93 , ASN A:97 , ARG A:137 , ASP A:139 , ARG A:148 , HOH A:198 , HOH A:200 , HOH A:208 , HOH A:212 , HOH A:215 , ALF A:499 , HOH A:727BINDING SITE FOR RESIDUE C5P A 196

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QF9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:91 -Pro A:92

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QF9)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADENYLATE_KINASEPS00113 Adenylate kinase signature.KCY_DICDI87-98  1A:86-97

(-) Exons   (0, 0)

(no "Exon" information available for 1QF9)

(-) 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:194
 aligned with KCY_DICDI | P20425 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:194
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191    
            KCY_DICDI     2 MEKSKPNVVFVLGGPGSGKGTQCANIVRDFGWVHLSAGDLLRQEQQSGSKDGEMIATMIKNGEIVPSIVTVKLLKNAIDANQGKNFLVDGFPRNEENNNSWEENMKDFVDTKFVLFFDCPEEVMTQRLLKRGESSGRSDDNIESIKKRFNTFNVQTKLVIDHYNKFDKVKIIPANRDVNEVYNDVENLFKSMGF 195
               SCOP domains d1qf9a_ A: UMP/CMP kinase                                                                                                                                                                          SCOP domains
               CATH domains 1qf9A00 A:1-194 P-loop containing nucleotide triphosphate hydrolases                                                                                                                               CATH domains
               Pfam domains ----------ADK-1qf9A01 A:11-168                                                                                                                                          -------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.....hhhhhhhhhhhh..eeeehhhhhhhhhh.....hhhhhhhhh......hhhhhhhhhhhhh......eeee.....hhhhhhhhhhh...eeeeeeeeee..hhhhhhhhhhhhh........hhhhhhhhhhhhh.hhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------ADENYLATE_KI------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qf9 A   1 MEKSKPNVVFVLGGPGSGKGTQCANIVRDFGWVHLSAGDLLRQEQQSGSKDGEMIATMIKNGEIVPSIVTVKLLKNAIDANQGKNFLVDGFPRNEENNNSWEENMKDFVDTKFVLFFDCPEEVMTQRLLKRGESSGRSDDNIESIKKRFNTFNVQTKLVIDHYNKFDKVKIIPANRDVNEVYNDVENLFKSMGF 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KCY_DICDI | P20425)
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: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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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:0016776    phosphotransferase activity, phosphate group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to a phosphate group (acceptor).
    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:0046705    CDP biosynthetic process    The chemical reactions and pathways resulting in the formation of CDP, cytidine (5'-)diphosphate.
    GO:0006225    UDP biosynthetic process    The chemical reactions and pathways resulting in the formation of UDP, uridine (5'-)diphosphate.
    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:0043173    nucleotide salvage    Any process which produces a nucleotide, a compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety, from derivatives of it without de novo synthesis.
    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:0043100    pyrimidine nucleobase salvage    Any process that generates pyrimidine nucleobases, 1,3-diazine organic nitrogenous bases, from derivatives of them without de novo synthesis.
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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

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

UniProtKB/Swiss-Prot
        KCY_DICDI | P20425: 1uke 2ukd 3ukd 4ukd 5ukd

(-) Related Entries Specified in the PDB File

1ukd 2ukd 4ukd 5ukd