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(-) Description

Title :  ADP AND DTDP BOUND CRYSTAL STRUCTURE OF THYMIDYLATE KINASE (AQ_969) FROM AQUIFEX AEOLICUS VF5
 
Authors :  A. Biswas, J. Jeyakanthan, K. Sekar, S. Kuramitsu, S. Yokoyama
Date :  04 Nov 16  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase, Transferase, Rossmann Fold, Product-Bound (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: A, B
    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  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CA2Ligand/IonCALCIUM ION
3MG6Ligand/IonMAGNESIUM ION
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5TYD2Ligand/IonTHYMIDINE-5'-DIPHOSPHATE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY 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 , TYD A:202 , MG A:203 , HOH A:313 , HOH A:319 , HOH A:329 , HOH A:340 , HOH A:344 , HOH A:345 , HOH A:346 , HOH A:350 , HOH A:397 , GLU B:177binding site for residue ADP A 201
02AC2SOFTWAREASP A:9 , LYS A:13 , GLU A:36 , ARG A:47 , PHE A:64 , ARG A:90 , THR A:95 , TYR A:98 , GLN A:99 , ARG A:145 , ADP A:201 , MG A:203 , MPD A:208 , HOH A:313 , HOH A:319 , HOH A:320 , HOH A:338 , HOH A:339 , HOH A:378binding site for residue TYD A 202
03AC3SOFTWARETHR A:14 , ADP A:201 , TYD A:202 , HOH A:313 , HOH A:319 , HOH A:339binding site for residue MG A 203
04AC4SOFTWAREGLU A:57 , LYS A:103 , HOH A:369 , HOH A:406 , HOH A:414 , HOH A:432binding site for residue MG A 204
05AC5SOFTWAREASN A:114 , HOH A:381 , HOH A:389binding site for residue MG A 205
06AC6SOFTWAREGLU A:142 , HOH A:374 , HOH A:397 , HOH A:427 , GLU B:177 , HOH B:414binding site for residue CA A 206
07AC7SOFTWAREGLU A:180 , HOH A:376 , HOH A:421 , HOH A:433 , ASP B:173 , SER B:175 , HOH B:393binding site for residue CA A 207
08AC8SOFTWARELEU A:50 , GLU A:60 , GLN A:99 , LYS A:103 , TYD A:202binding site for residue MPD A 208
09AC9SOFTWAREGLY B:10 , SER B:11 , GLY B:12 , LYS B:13 , THR B:14 , THR B:15 , ARG B:139 , LYS B:143 , ARG B:145 , GLY B:176 , GLU B:177 , GLU B:178 , TYD B:202 , MG B:203 , HOH B:315 , HOH B:332 , HOH B:337 , HOH B:359 , HOH B:371 , HOH B:395binding site for residue ADP B 201
10AD1SOFTWAREASP B:9 , LYS B:13 , GLU B:36 , ARG B:47 , PHE B:64 , ARG B:90 , THR B:95 , TYR B:98 , GLN B:99 , ARG B:145 , ADP B:201 , MG B:203 , MPD B:206 , HOH B:316 , HOH B:331 , HOH B:332 , HOH B:337 , HOH B:348 , HOH B:377binding site for residue TYD B 202
11AD2SOFTWARETHR B:14 , ADP B:201 , TYD B:202 , HOH B:332 , HOH B:337 , HOH B:377binding site for residue MG B 203
12AD3SOFTWAREGLU B:57 , LYS B:103 , HOH B:322 , HOH B:403 , HOH B:406binding site for residue MG B 204
13AD4SOFTWAREASN B:114 , HOH B:340 , HOH B:378binding site for residue MG B 205
14AD5SOFTWARELEU B:50 , GLN B:99 , LYS B:103 , TYD B:202binding site for residue MPD B 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H56)

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H56)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H56)

(-) Exons   (0, 0)

(no "Exon" information available for 5H56)

(-) 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.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h56 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:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h56 B   1 MLIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYREPGGTKVGEVLREILLTEELDERTELLLFEASRSKLIEEKIIPDLKRDKVVILDRFVLSTIAYQGYGKGLDVEFIKNLNEFATRGVKPDITLLLDIPVDIALRRLKEKNRFENKEFLEKVRKGFLELAKEEENVVVIDASGEEEEVFKEILRALSGVLRV 195
                                    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)
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  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 5H56)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H56)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H56)

(-) 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 ]  
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 Related Entries

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        KTHY_AQUAE | O67099: 2pbr 4s2e 4s35 5h5b 5h5k 5xai 5xb2 5xb3 5xb5 5xbh

(-) Related Entries Specified in the PDB File

5h5b 5h5k