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(-) Description

Title :  ADP-MG-F-DTMP BOUND CRYSTAL STRUCTURE OF THYMIDYLATE KINASE (AQ_969) FROM AQUIFEX AEOLICUS VF5
 
Authors :  A. Biswas, J. Jeyakanthan, K. Sekar
Date :  15 Mar 17  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase, Tranferase, Complex, Nucleotide Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Biswas, J. Jeyakanthan, K. Sekar, S. Kuramitsu, S. Yokoyama
Structural Studies Of A Hyperthermophilic Thymidylate Kinas Enzyme Reveal Conformational Sub-States Along The Reaction Coordinate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THYMIDYLATE KINASE
    Chains: B, A
    EC Number: 2.7.4.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TMK, AQ_969
    Organism Scientific: AQUIFEX AEOLICUS (STRAIN VF5)
    Organism Taxid: 224324
    Strain: VF5
    Synonym: DTMP KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2F3Ligand/IonFLUORIDE ION
3MG1Ligand/IonMAGNESIUM ION
4TMP2Ligand/IonTHYMIDINE-5'-PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:10 , SER B:11 , GLY B:12 , LYS B:13 , THR B:14 , THR B:15 , ARG B:139 , ARG B:145 , GLY B:176 , GLU B:177 , GLU B:178 , MG B:203 , F B:204 , F B:205 , HOH B:308 , HOH B:329 , HOH B:333binding site for residue ADP B 201
2AC2SOFTWAREASP B:9 , GLU B:36 , ARG B:47 , PHE B:64 , ARG B:68 , ARG B:90 , THR B:95 , TYR B:98 , GLN B:99 , ARG B:145 , MG B:203 , F B:204 , F B:205 , F B:206 , HOH B:308 , HOH B:346 , HOH B:353binding site for residue TMP B 202
3AC3SOFTWARETHR B:14 , ASP B:89 , ADP B:201 , TMP B:202 , F B:204 , F B:205 , F B:206binding site for residue MG B 203
4AC4SOFTWARELYS B:13 , THR B:14 , ASP B:89 , ADP B:201 , TMP B:202 , MG B:203binding site for residue F B 204
5AC5SOFTWARETHR B:14 , ARG B:145 , ADP B:201 , TMP B:202 , MG B:203binding site for residue F B 205
6AC6SOFTWARETHR B:14 , ASP B:89 , TMP B:202 , MG B:203 , HOH B:348binding site for residue F B 206
7AC7SOFTWAREGLY A:10 , SER A:11 , GLY A:12 , LYS A:13 , THR A:14 , THR A:15 , ARG A:139 , LYS A:143 , ARG A:145 , GLY A:176 , GLU A:177 , GLU A:178 , HOH A:320 , HOH A:336binding site for residue ADP A 201
8AC8SOFTWAREASP A:9 , GLU A:36 , ARG A:47 , PHE A:64 , ARG A:68 , ARG A:90 , THR A:95 , TYR A:98 , GLN A:99 , ARG A:145 , HOH A:320binding site for residue TMP A 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5XB2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu B:36 -Pro B:37
2Glu A:36 -Pro A:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5XB2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5XB2)

(-) Exons   (0, 0)

(no "Exon" information available for 5XB2)

(-) 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
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xb2 A   1 MLIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYREPGGTKVGEVLREILLTEELDERTELLLFEASRSKLIEEKIIPDLKRDKVVILDRFVLSTIAYQGYGKGLDVEFIKNLNEFATRGVKPDITLLLDIPVDIALRRLKEKNRFENKEFLEKVRKGFLELAKEEENVVVIDASGEEEEVFKEILRALSGVLR 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    


Chain B from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xb2 B   1 MLIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYREPGGTKVGEVLREILLTEELDERTELLLFEASRSKLIEEKIIPDLKRDKVVILDRFVLSTIAYQGYGKGLDVEFIKNLNEFATRGVKPDITLLLDIPVDIALRRLKEKNRFENKEFLEKVRKGFLELAKEEENVVVIDASGEEEEVFKEILRALSGVLR 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  (0, 0)

(no "SCOP Domain" information available for 5XB2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5XB2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5XB2)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:36 - Pro A:37   [ RasMol ]  
    Glu B:36 - Pro B:37   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        KTHY_AQUAE | O67099: 2pbr 4s2e 4s35 5h56 5h5b 5h5k 5xai 5xb3 5xb5 5xbh

(-) Related Entries Specified in the PDB File

5xai 5xb3 5xb5 5xbh