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(-) Description

Title :  CYTIDINE MONOPHOSPHATE KINASE IN COMPLEX WITH CYTIDINE-DI-PHOSPHATE
 
Authors :  B. Golinelli-Pimpaneau, P. Briozzo
Date :  19 Sep 98  (Deposition) - 20 Sep 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Nucleotide Monophosphate Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Briozzo, B. Golinelli-Pimpaneau, A. M. Gilles, J. F. Gaucher, S. Burlacu-Miron, H. Sakamoto, J. Janin, O. Barzu
Structures Of Escherichia Coli Cmp Kinase Alone And In Complex With Cdp: A New Fold Of The Nucleoside Monophosphate Binding Domain And Insights Into Cytosine Nucleotide Specificity.
Structure V. 6 1517 1998
PubMed-ID: 9862805  |  Reference-DOI: 10.1016/S0969-2126(98)00150-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (CYTIDINE MONOPHOSPHATE KINASE)
    Chains: A
    EC Number: 2.7.4.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: DOMAIN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CDP1Ligand/IonCYTIDINE-5'-DIPHOSPHATE
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:13 , GLY A:15 , ALA A:16 , GLY A:17 , LYS A:18 , GLY A:19 , HOH A:408 , HOH A:432 , HOH A:445BINDING SITE FOR RESIDUE SO4 A 228
2AC2SOFTWAREGLY A:17 , THR A:20 , HIS A:51 , ILE A:209 , HOH A:430 , HOH A:434 , HOH A:469BINDING SITE FOR RESIDUE SO4 A 229
3AC3SOFTWARESER A:14 , SER A:36 , GLY A:37 , ARG A:41 , SER A:101 , ARG A:110 , GLY A:130 , ARG A:131 , ASP A:132 , ASP A:185 , ARG A:188 , HOH A:408 , HOH A:419 , HOH A:423 , HOH A:445 , HOH A:461BINDING SITE FOR RESIDUE CDP A 407

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:123 -Pro A:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CMK)

(-) 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:221
 aligned with KCY_ECOLI | P0A6I0 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:221
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 
            KCY_ECOLI     3 AIAPVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHHHVDVASEDALVPLASHLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAASQVAAFPRVREALLRRQRAFRELPGLIADGRDMGTVVFPDAPVKIFLDASSEERAHRRMLQLQEKGFSVNFERLLAEIKERDDRDRNRAVAPLVPAADALVLDSTTLSIEQVIEKALQYARQK 223
               SCOP domains d2cmka_ A: CMP kinase                                                                                                                                                                                                         SCOP domains
               CATH domains 2cmkA00 A:3-223 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhh..eeeehhhhhhhhhhhhhh.......hhhhhhhhhh..eeee......eeee.......hhh.hhhhhhhhhhhh.hhhhhhhhhhhhhh....eeeeee............eeeeee..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.............eeee.....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cmk A   3 AIAPVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHHHVDVASEDALVPLASHLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAASQVAAFPRVREALLRRQRAFRELPGLIADGRDMGTVVFPDAPVKIFLDASSEERAHRRMLQLQEKGFSVNFERLLAEIKERDDRDRNRAVAPLVPAADALVLDSTTLSIEQVIEKALQYARQK 223
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
   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  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KCY_ECOLI | P0A6I0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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.
biological process
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0015949    nucleobase-containing small molecule interconversion    The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
    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:0006220    pyrimidine nucleotide metabolic process    The chemical reactions and pathways involving 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KCY_ECOLI | P0A6I0: 1cke 1kdo 1kdp 1kdr 1kdt 2fem 2feo

(-) Related Entries Specified in the PDB File

1cke