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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS CYTIDINE MONOPHOSPHATE KINASE IN COMPLEX WITH CYTIDINE-5'-MONOPHOSPHATE
 
Authors :  B. Dhaliwal
Date :  08 Jun 06  (Deposition) - 08 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Rossmann Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Dhaliwal, J. Ren, M. Lockyer, I. Charles, A. R. Hawkins, D. K. Stammers
Structure Of Staphylococcus Aureus Cytidine Monophosphate Kinase In Complex With Cytidine 5'-Monophosphate.
Acta Crystallogr. , Sect. F V. 62 710 2006
PubMed-ID: 16880539  |  Reference-DOI: 10.1107/S174430910602447X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTIDYLATE KINASE
    Chains: A, B, C
    EC Number: 2.7.4.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CMK
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: CYTIDINE MONOPHOSPHATE KINASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1C5P3Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2PG41Ligand/IonTETRAETHYLENE GLYCOL
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1C5P1Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2PG4-1Ligand/IonTETRAETHYLENE GLYCOL
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1C5P1Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2PG41Ligand/IonTETRAETHYLENE GLYCOL
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1C5P1Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2PG4-1Ligand/IonTETRAETHYLENE GLYCOL
3SO41Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:13 , ALA A:14 , GLY A:15 , LYS A:16 , SER A:17 , HOH A:1478BINDING SITE FOR RESIDUE SO4 A 1400
2AC2SOFTWAREALA B:13 , ALA B:14 , GLY B:15 , LYS B:16 , SER B:17 , ARG B:153 , HOH B:1402 , HOH B:1438BINDING SITE FOR RESIDUE SO4 B 1401
3AC3SOFTWAREALA C:13 , ALA C:14 , GLY C:15 , LYS C:16 , SER C:17 , ARG C:153BINDING SITE FOR RESIDUE SO4 C 1402
4AC4SOFTWARETHR A:34 , GLY A:35 , TYR A:38 , ARG A:39 , VAL A:95 , SER A:96 , ARG A:105 , GLY A:125 , ARG A:126 , ASP A:127 , ILE A:128 , ARG A:176 , ASP A:180 , ARG A:183 , HOH A:1402 , HOH A:1404 , HOH A:1405BINDING SITE FOR RESIDUE C5P A 1300
5AC5SOFTWARETHR B:34 , GLY B:35 , TYR B:38 , ARG B:39 , VAL B:95 , SER B:96 , ALA B:99 , ARG B:105 , GLY B:125 , ARG B:126 , ASP B:127 , ARG B:176 , ASP B:180 , ARG B:183 , HOH B:1402 , HOH B:1406 , HOH B:1444 , HOH B:1493BINDING SITE FOR RESIDUE C5P B 1301
6AC6SOFTWARELYS C:16 , THR C:34 , GLY C:35 , TYR C:38 , ARG C:39 , VAL C:95 , SER C:96 , ALA C:99 , ARG C:105 , GLY C:125 , ARG C:126 , ASP C:127 , ARG C:176 , ASP C:180 , ARG C:183 , HOH C:1407 , HOH C:1413 , HOH C:1426 , HOH C:1494BINDING SITE FOR RESIDUE C5P C 1302
7AC7SOFTWAREMET B:29 , ILE B:30 , TYR B:67 , LYS B:68 , ALA B:69 , LYS B:71 , LYS B:119 , GLY B:120 , ILE B:121 , HOH B:1492BINDING SITE FOR RESIDUE PG4 B 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H92)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2H92)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H92)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2H92)

(-) Exons   (0, 0)

(no "Exon" information available for 2H92)

(-) 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:216
 aligned with KCY_STAAW | P63807 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
            KCY_STAAW     3 AINIALDGPAAAGKSTIAKRVASELSMIYVDTGAMYRALTYKYLKLNKTEDFAKLVDQTTLDLTYKADKGQCVILDNEDVTDFLRNNDVTQHVSYVASKEPVRSFAVKKQKELAAEKGIVMDGRDIGTVVLPDADLKVYMIASVEERAERRYKDNQLRGIESNFEDLKRDIEARDQYDMNREISPLRKADDAVTLDTTGKSIEEVTDEILAMVSQI 218
               SCOP domains d2h92a_ A: CMP kinase                                                                                                                                                                                                    SCOP domains
               CATH domains 2h92A00 A:3-218 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh....hhhhhhhh..eeeee.....eeeee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee............eeeeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...........eeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2h92 A   3 AINIALDGPAAAGKSTIAKRVASELSMIYVDTGAMYRALTYKYLKLNKTEDFAKLVDQTTLDLTYKADKGQCVILDNEDVTDFLRNNDVTQHVSYVASKEPVRSFAVKKQKELAAEKGIVMDGRDIGTVVLPDADLKVYMIASVEERAERRYKDNQLRGIESNFEDLKRDIEARDQYDMNREISPLRKADDAVTLDTTGKSIEEVTDEILAMVSQI 218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      


Chain B from PDB  Type:PROTEIN  Length:216
 aligned with KCY_STAAW | P63807 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
            KCY_STAAW     3 AINIALDGPAAAGKSTIAKRVASELSMIYVDTGAMYRALTYKYLKLNKTEDFAKLVDQTTLDLTYKADKGQCVILDNEDVTDFLRNNDVTQHVSYVASKEPVRSFAVKKQKELAAEKGIVMDGRDIGTVVLPDADLKVYMIASVEERAERRYKDNQLRGIESNFEDLKRDIEARDQYDMNREISPLRKADDAVTLDTTGKSIEEVTDEILAMVSQI 218
               SCOP domains d2h92b_ B: CMP kinase                                                                                                                                                                                                    SCOP domains
               CATH domains 2h92B00 B:3-218 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh....hhhhhhhh..eeeee.....eeeee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee............eeeeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...........eeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2h92 B   3 AINIALDGPAAAGKSTIAKRVASELSMIYVDTGAMYRALTYKYLKLNKTEDFAKLVDQTTLDLTYKADKGQCVILDNEDVTDFLRNNDVTQHVSYVASKEPVRSFAVKKQKELAAEKGIVMDGRDIGTVVLPDADLKVYMIASVEERAERRYKDNQLRGIESNFEDLKRDIEARDQYDMNREISPLRKADDAVTLDTTGKSIEEVTDEILAMVSQI 218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      


Chain C from PDB  Type:PROTEIN  Length:216
 aligned with KCY_STAAW | P63807 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
            KCY_STAAW     3 AINIALDGPAAAGKSTIAKRVASELSMIYVDTGAMYRALTYKYLKLNKTEDFAKLVDQTTLDLTYKADKGQCVILDNEDVTDFLRNNDVTQHVSYVASKEPVRSFAVKKQKELAAEKGIVMDGRDIGTVVLPDADLKVYMIASVEERAERRYKDNQLRGIESNFEDLKRDIEARDQYDMNREISPLRKADDAVTLDTTGKSIEEVTDEILAMVSQI 218
               SCOP domains d2h92c_ C: CMP kinase                                                                                                                                                                                                    SCOP domains
               CATH domains 2h92C00 C:3-218 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhh....hhhhhhhh..eeeee.....eeeee..ee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee............eeeeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...........eeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2h92 C   3 AINIALDGPAAAGKSTIAKRVASELSMIYVDTGAMYRALTYKYLKLNKTEDFAKLVDQTTLDLTYKADKGQCVILDNEDVTDFLRNNDVTQHVSYVASKEPVRSFAVKKQKELAAEKGIVMDGRDIGTVVLPDADLKVYMIASVEERAERRYKDNQLRGIESNFEDLKRDIEARDQYDMNREISPLRKADDAVTLDTTGKSIEEVTDEILAMVSQI 218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212
   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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H92)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (KCY_STAAW | P63807)
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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  2h92
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  KCY_STAAW | P63807
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