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(-) Description

Title :  AMPPCP AND TMP BOUND CRYSTAL STRUCTURE OF THYMIDYLATE KINASE (AQ_969) FROM AQUIFEX AEOLICUS VF5
 
Authors :  A. Biswas, J. Jeyakanthan, K. Sekar, S. Kuramitsu, S. Yokoyama
Date :  26 Jan 15  (Deposition) - 27 Jan 16  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Atp Binding, Tmp Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Biswas, J. Jeyakanthan, K. Sekar
Structural Studies Of A Hyperthermophilic Thymidylate Kinas Enzyme Reveal Conformational Sub-States Along The Reaction Coordinate
Febs J. 2017
PubMed: search

(-) Compounds

Molecule 1 - THYMIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21-CODONPLUS (DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AQ_969, TMK
    Organism Scientific: AQUIFEX AEOLICUS
    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, 11)

Asymmetric/Biological Unit (5, 11)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2CL1Ligand/IonCHLORIDE ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4MG4Ligand/IonMAGNESIUM ION
5TMP2Ligand/IonTHYMIDINE-5'-PHOSPHATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:9 , GLY A:10 , SER A:11 , GLY A:12 , LYS A:13 , THR A:14 , THR A:15 , ARG A:90 , ARG A:139 , GLU A:147 , GLY A:176 , GLU A:178 , TMP A:202 , MG A:203 , HOH A:301 , HOH A:302 , HOH A:303 , HOH A:397 , HOH A:398 , HOH A:399 , HOH A:404 , HOH A:407 , HOH A:408 , HOH A:485BINDING SITE FOR RESIDUE ACP A 201
02AC2SOFTWAREASP A:9 , GLU A:36 , PRO A:37 , ARG A:47 , PHE A:64 , ARG A:90 , THR A:95 , TYR A:98 , GLN A:99 , ASN A:144 , PHE A:146 , ACP A:201 , HOH A:302 , HOH A:303 , HOH A:408 , HOH A:409 , HOH A:457BINDING SITE FOR RESIDUE TMP A 202
03AC3SOFTWARETHR A:14 , ACP A:201 , HOH A:301 , HOH A:302 , HOH A:303BINDING SITE FOR RESIDUE MG A 203
04AC4SOFTWARETYR A:29 , PHE A:30 , ASP A:83 , ASN A:148 , GLU A:150BINDING SITE FOR RESIDUE MG A 204
05AC5SOFTWAREASP A:134 , ILE A:135 , ARG A:138 , HOH A:359BINDING SITE FOR RESIDUE EDO A 205
06AC6SOFTWAREASP B:9 , GLY B:10 , SER B:11 , GLY B:12 , LYS B:13 , THR B:14 , THR B:15 , ARG B:90 , ARG B:139 , GLU B:147 , GLY B:176 , GLU B:177 , GLU B:178 , TMP B:202 , MG B:203 , HOH B:301 , HOH B:302 , HOH B:303 , HOH B:323 , HOH B:369 , HOH B:372 , HOH B:374 , HOH B:375 , HOH B:376BINDING SITE FOR RESIDUE ACP B 201
07AC7SOFTWAREASP B:9 , GLU B:36 , PRO B:37 , ARG B:47 , PHE B:64 , ARG B:90 , THR B:95 , TYR B:98 , GLN B:99 , ASN B:144 , PHE B:146 , ACP B:201 , HOH B:301 , HOH B:303 , HOH B:323 , HOH B:358BINDING SITE FOR RESIDUE TMP B 202
08AC8SOFTWARETHR B:14 , ACP B:201 , HOH B:301 , HOH B:302 , HOH B:303BINDING SITE FOR RESIDUE MG B 203
09AC9SOFTWAREVAL B:133 , GLU B:153 , ARG B:156BINDING SITE FOR RESIDUE MG B 204
10BC1SOFTWAREASN B:114BINDING SITE FOR RESIDUE CL B 205
11BC2SOFTWAREVAL A:195 , GLU B:179BINDING SITE FOR RESIDUE EDO B 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4S35)

(-) 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 4S35)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S35)

(-) Exons   (0, 0)

(no "Exon" information available for 4S35)

(-) 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: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.hhhhhhhh........hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s35 A   1 MLIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYREPGGTKVGEVLREILLTEELDERTELLLFEASRSKLIEEKIIPDLKRDKVVILDRFVLSTIAYQGYGKGLDVEFIKNLNEFATRGVKPDITLLLDIPVDIALRRLKEKNRFENKEFLEKVRKGFLELAKEEENVVVIDASGEEEEVFKEILRALSGVLRV 195
                                    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.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s35 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 4S35)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S35)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S35)

(-) 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

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

UniProtKB/Swiss-Prot
        KTHY_AQUAE | O67099: 2pbr 4s2e 5h56 5h5b 5h5k 5xai 5xb2 5xb3 5xb5 5xbh

(-) Related Entries Specified in the PDB File

2pbr THE SAME PROTEIN FROM AQUIFEX AEOLICUS VF5 IN SULFATE BOUND FORM