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(-) Description

Title :  CYTIDINE MONOPHOSPHATE KINASE FROM E.COLI IN COMPLEX WITH 2',3'-DIDEOXY-CYTIDINE MONOPHOSPHATE
 
Authors :  T. Bertrand, P. Briozzo, L. Assairi, A. Ofiteru, N. Bucurenci, H. Munier-Lehmann, B. Golinelli-Pimpaneau, O. Barzu, A. M. Gilles
Date :  13 Nov 01  (Deposition) - 22 Jan 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nucleotide Monophosphate Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Bertrand, P. Briozzo, L. Assairi, A. Ofiteru, N. Bucurenci, H. Munier-Lehmann, B. Golinelli-Pimpaneau, O. Barzu, A. M. Gilles
Sugar Specificity Of Bacterial Cmp Kinases As Revealed By Crystal Structures And Mutagenesis Of Escherichia Coli Enzyme.
J. Mol. Biol. V. 315 1099 2002
PubMed-ID: 11827479  |  Reference-DOI: 10.1006/JMBI.2001.5286
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTIDYLATE KINASE
    ChainsA, B
    EC Number2.7.4.14
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPHSP210
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneCMK
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymCYTIDINE MONOPHOSPHATE KINASE;
CK;
CMP 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, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1DOC2Mod. Residue2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1DOC1Mod. Residue2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1DOC1Mod. Residue2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
2SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:15 , ALA A:16 , GLY A:17 , LYS A:18 , GLY A:19 , HOH A:5448 , HOH A:5454BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREGLY A:17 , THR A:20 , HIS A:51 , HOH A:5419 , HOH A:5421 , HOH A:5423 , HOH A:5474BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWAREPRO B:13 , SER B:14 , GLY B:15 , ALA B:16 , GLY B:17 , LYS B:18 , GLY B:19 , HOH B:6447 , HOH B:6454 , HOH B:6490 , HOH B:6582BINDING SITE FOR RESIDUE SO4 B 601
4AC4SOFTWARESER A:36 , GLY A:37 , TYR A:40 , ARG A:41 , ALA A:104 , ARG A:110 , GLY A:130 , ARG A:131 , ASP A:132 , ARG A:188 , HOH A:5439 , HOH A:5448 , HOH A:5456 , HOH A:5468 , HOH A:5508BINDING SITE FOR RESIDUE DOC A 5407
5AC5SOFTWARESER B:14 , SER B:36 , GLY B:37 , TYR B:40 , ARG B:41 , ALA B:100 , SER B:101 , ALA B:104 , ARG B:110 , GLY B:130 , ARG B:131 , ASP B:132 , HOH B:6411 , HOH B:6415 , HOH B:6419 , HOH B:6453 , HOH B:6454 , HOH B:6456 , HOH B:6627BINDING SITE FOR RESIDUE DOC B 6407

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:123 -Pro A:124
2Leu B:123 -Pro B:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KDT)

(-) 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:223
 aligned with KCY_ECOLI | P0A6I0 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:223
                                    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 AIAPVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHHHVDVASEDALVPLASHLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAASQVAAFPRVREALLRRQRAFRELPGLIADGRDMGTVVFPDAPVKIFLDASSEERAHRRMLQLQEKGFSVNFERLLAEIKERDDRDRNRAVAPLVPAADALVLDSTTLSIEQVIEKALQYARQKLA 225
               SCOP domains d1kdta_ A: CMP kinase                                                                                                                                                                                                           SCOP domains
               CATH domains 1kdtA00 A:3-225 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhh.....hhhhhhhhhhh..eeee......eeee..ee..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......eeeee............eeeeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh............eeee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kdt A   3 AIAPVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHHHVDVASEDALVPLASHLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAASQVAAFPRVREALLRRQRAFRELPGLIADGRDMGTVVFPDAPVKIFLDASSEERAHRRMLQLQEKGFSVNFERLLAEIKERDDRDRNRAVAPLVPAADALVLDSTTLSIEQVIEKALQYARQKLA 225
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   

Chain B from PDB  Type:PROTEIN  Length:223
 aligned with KCY_ECOLI | P0A6I0 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:223
                                    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 AIAPVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHHHVDVASEDALVPLASHLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAASQVAAFPRVREALLRRQRAFRELPGLIADGRDMGTVVFPDAPVKIFLDASSEERAHRRMLQLQEKGFSVNFERLLAEIKERDDRDRNRAVAPLVPAADALVLDSTTLSIEQVIEKALQYARQKLA 225
               SCOP domains d1kdtb_ B: CMP kinase                                                                                                                                                                                                           SCOP domains
               CATH domains 1kdtB00 B:3-225 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                            CATH domains
           Pfam domains (1) ----------------------------------------------------------Cytidylate_kin-1kdtB01 B:61-218                                                                                                                               ------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------Cytidylate_kin-1kdtB02 B:61-218                                                                                                                               ------- Pfam domains (2)
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhh.....hhhhhhhhhhh..eeee......eeee..ee..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......eeeee............eeeeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...........eeee....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kdt B   3 AIAPVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHHHVDVASEDALVPLASHLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAASQVAAFPRVREALLRRQRAFRELPGLIADGRDMGTVVFPDAPVKIFLDASSEERAHRRMLQLQEKGFSVNFERLLAEIKERDDRDRNRAVAPLVPAADALVLDSTTLSIEQVIEKALQYARQKLA 225
                                    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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 | P0A6I01cke 1kdo 1kdp 1kdr 2cmk 2fem 2feo

(-) Related Entries Specified in the PDB File

1kdo 1kdp 1kdr