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(-) Description

Title :  CRYSTAL STRUCTURE OF CYTIDYLATE KINASE (CMK) FROM MYCOBACTERIUM ABSCESSUS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  23 Mar 11  (Deposition) - 30 Mar 11  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Mycobacterium, Tuberculosis, Water Contaminant, Chronic Lung Disease, Rapid Growing Mycobacterium, Pyrimidine Nucleoside Monophosphate Kinase, Phosphotransferase, , Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
PubMed-ID: 25613812  |  Reference-DOI: 10.1016/J.TUBE.2014.12.003

(-) Compounds

Molecule 1 - CYTIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAVA0421
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CMK, MAB_2371
    Organism Scientific: MYCOBACTERIUM ABSCESSUS
    Organism Taxid: 561007
    Strain: ATCC 19977 / DSM 44196
    Synonym: CK, CYTIDINE MONOPHOSPHATE KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3R8C)

(-) Sites  (0, 0)

(no "Site" information available for 3R8C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R8C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3R8C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R8C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R8C)

(-) Exons   (0, 0)

(no "Exon" information available for 3R8C)

(-) 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:198
 aligned with B1MB31_MYCA9 | B1MB31 from UniProtKB/TrEMBL  Length:223

    Alignment length:220
                              1                                                                                                                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218
         B1MB31_MYCA9     - --MVAVDGPSGTGKSSVAKELARQLGASYLDTGAMYRIVTLWVLRAGVDLTDPAAIAAATDQVPMSVSSDPDAQTALLAGEDVSVPIRGNEVTGAVSAVSAVPAVRERLVRQQRELAESSGAVVVEGRDIGTVVLPDADVKIYLTASAQARAQRRNAQNVSGGGDDEYEKVLADVQRRDHLDSTRAVSPLRPAEDALEVDTSDMTQEQVVAHLLDLVRTR 218
               SCOP domains d3r8ca_ A: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhh....hhhhhhhhh....ee..........ee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.............eeeeee.hhhhhhhhhh---------------hhhhhhhhhh-------........eeee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r8c A  -1 SMVVAVDGPSGTGKSSVAKELARQLGASYLDTGAMYRIVTLWVLRAGVDLTDPAAIAAATDQVPMSVSSDPDAQTALLAGEDVSVPIRGNEVTGAVSAVSAVPAVRERLVRQQRELAESSGAVVVEGRDIGTVVLPDADVKIYLTASAQARAQRRN---------------LADVQRRDHL-------PLRPAEDALEVDTSDMTQEQVVAHLLDLVRTR 218
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148     |   -         - |     178|      188       198       208       218
                                                                                                                                                                                     154             170      179     187                               


Chain B from PDB  Type:PROTEIN  Length:205
 aligned with B1MB31_MYCA9 | B1MB31 from UniProtKB/TrEMBL  Length:223

    Alignment length:220
                              1                                                                                                                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218
         B1MB31_MYCA9     - --MVAVDGPSGTGKSSVAKELARQLGASYLDTGAMYRIVTLWVLRAGVDLTDPAAIAAATDQVPMSVSSDPDAQTALLAGEDVSVPIRGNEVTGAVSAVSAVPAVRERLVRQQRELAESSGAVVVEGRDIGTVVLPDADVKIYLTASAQARAQRRNAQNVSGGGDDEYEKVLADVQRRDHLDSTRAVSPLRPAEDALEVDTSDMTQEQVVAHLLDLVRTR 218
               SCOP domains d3r8cb_ B: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------Cytidylate_kin-3r8cB01 B:55-213                                                                                                                                ----- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------Cytidylate_kin-3r8cB02 B:55-213                                                                                                                                ----- Pfam domains (2)
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhh....hhhhhhhh.....eee........eee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.............eeeeee.hhhhhhhhhh---------------hhhhhhhhhhhhhh...........eeee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r8c B  -1 SMVVAVDGPSGTGKSSVAKELARQLGASYLDTGAMYRIVTLWVLRAGVDLTDPAAIAAATDQVPMSVSSDPDAQTALLAGEDVSVPIRGNEVTGAVSAVSAVPAVRERLVRQQRELAESSGAVVVEGRDIGTVVLPDADVKIYLTASAQARAQRRN---------------LADVQRRDHLDSTRAVSPLRPAEDALEVDTSDMTQEQVVAHLLDLVRTR 218
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148     |   -         - |     178       188       198       208       218
                                                                                                                                                                                     154             170
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R8C)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B1MB31_MYCA9 | B1MB31)
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: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.

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 Related Entries

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

UniProtKB/TrEMBL
        B1MB31_MYCA9 | B1MB31: 4die

(-) Related Entries Specified in the PDB File

3r20 SAME PROTEIN FROM MYCOBACTERIUM SMEGMATIS RELATED ID: MYABA.00663.A RELATED DB: TARGETDB