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(-) Description

Title :  CRYSTAL STRUCTURE OF EHV4-TK COMPLEXED WITH THY AND SO4
 
Authors :  A. Gardberg, L. Shuvalova, C. Monnerjahn, M. Konrad, A. Lavie
Date :  30 Apr 03  (Deposition) - 04 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  P-Loop, Lid, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Gardberg, L. Shuvalova, C. Monnerjahn, M. Konrad, A. Lavie
Structural Basis For The Dual Thymidine And Thymidylate Kinase Activity Of Herpes Thymidine Kinases.
Structure V. 11 1265 2003
PubMed-ID: 14527394  |  Reference-DOI: 10.1016/J.STR.2003.09.003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THYMIDINE KINASE
    Chains: A, B
    EC Number: 2.7.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUT699
    Expression System Strain: BL21 C41 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TK
    Organism Common: EQUINE HERPESVIRUS 4
    Organism Scientific: EQUID HERPESVIRUS 4
    Organism Taxid: 10331
    Strain: 1942

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
2THM2Ligand/IonTHYMIDINE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
2THM2Ligand/IonTHYMIDINE
Biological Unit 2 (2, 16)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION
2THM4Ligand/IonTHYMIDINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:34 , GLY A:35 , ILE A:36 , GLY A:37 , LYS A:38 , SER A:39 , HOH A:840 , HOH A:844 , HOH A:849 , HOH A:856 , HOH A:1005BINDING SITE FOR RESIDUE SO4 A 801
2AC2SOFTWARETYR B:34 , GLY B:35 , ILE B:36 , GLY B:37 , LYS B:38 , SER B:39 , ARG B:196 , HOH B:841 , HOH B:852 , HOH B:941BINDING SITE FOR RESIDUE SO4 B 802
3AC3SOFTWAREPHE A:69 , GLU A:70 , THR A:71 , ARG A:104 , HOH A:805 , SER B:159 , HOH B:833BINDING SITE FOR RESIDUE SO4 A 803
4AC4SOFTWAREARG A:172 , PRO A:174 , GLN A:175BINDING SITE FOR RESIDUE SO4 A 804
5AC5SOFTWARESER A:159 , CYS A:161 , GLU A:275 , PHE B:69 , GLU B:70 , THR B:71 , ARG B:104 , HOH B:864BINDING SITE FOR RESIDUE SO4 B 805
6AC6SOFTWAREARG B:172 , PRO B:174 , GLN B:175 , HOH B:954BINDING SITE FOR RESIDUE SO4 B 806
7AC7SOFTWARETYR A:34 , GLU A:60 , ILE A:74 , TYR A:78 , GLN A:102 , PHE A:105 , ARG A:139 , SER A:144 , PHE A:148 , HOH A:824 , HOH A:825 , HOH A:1041BINDING SITE FOR RESIDUE THM A 701
8AC8SOFTWARETYR B:34 , GLU B:60 , TRP B:65 , ILE B:74 , GLN B:102 , PHE B:105 , SER B:144 , PHE B:148 , GLU B:201 , HOH B:831 , HOH B:838 , HOH B:1003BINDING SITE FOR RESIDUE THM B 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P6X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1P6X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P6X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P6X)

(-) Exons   (0, 0)

(no "Exon" information available for 1P6X)

(-) 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:333
 aligned with KITH_EHV4 | P24425 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:333
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349   
            KITH_EHV4    20 RRQVTIVRIYLDGVYGIGKSTTGRVMASAASGGSPTLYFPEPMAYWRTLFETDVISGIYDTQNRKQQGNLAVDDAALITAHYQSRFTTPYLILHDHTCTLFGGNSLQRGTQPDLTLVFDRHPVASTVCFPAARYLLGDMSMCALMAMVATLPREPQGGNIVVTTLNVEEHIRRLRTRARIGEQIDITLIATLRNVYFMLVNTCHFLRSGRVWRDGWGELPTSCGAYKHRATQMDAFQERVSPELGDTLFALFKTQELLDDRGVILEVHAWALDALMLKLRNLNVFSADLSGTPRQCAAVVESLLPLMSSTLSDFDSASALERAARTFNAEMGV 352
               SCOP domains d1p6xa_ A: Thymidine kinase                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1p6xA00 A:20-352 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.....hhhhhhhhhhhhhhh...eeee..hhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.......eeeeee..hhhhhhhhhhhhhhh...hhhhhhhhhh........eeeeeee.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhh...........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p6x A  20 SHMVTIVRIYLDGVYGIGKSTTGRVMASAASGGSPTLYFPEPMAYWRTLFETDVISGIYDTQNRKQQGNLAVDDAALITAHYQSRFTTPYLILHDHTCTLFGGNSLQRGTQPDLTLVFDRHPVASTVCFPAARYLLGDMSMCALMAMVATLPREPQGGNIVVTTLNVEEHIRRLRTRARIGEQIDITLIATLRNVYFMLVNTCHFLRSGRVWRDGWGELPTSCGAYKHRATQMDAFQERVSPELGDTLFALFKTQELLDDRGVILEVHAWALDALMLKLRNLNVFSADLSGTPRQCAAVVESLLPLMSSTLSDFDSASALERAARTFNAEMGV 352
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349   


Chain B from PDB  Type:PROTEIN  Length:331
 aligned with KITH_EHV4 | P24425 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:331
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 
            KITH_EHV4    21 RQVTIVRIYLDGVYGIGKSTTGRVMASAASGGSPTLYFPEPMAYWRTLFETDVISGIYDTQNRKQQGNLAVDDAALITAHYQSRFTTPYLILHDHTCTLFGGNSLQRGTQPDLTLVFDRHPVASTVCFPAARYLLGDMSMCALMAMVATLPREPQGGNIVVTTLNVEEHIRRLRTRARIGEQIDITLIATLRNVYFMLVNTCHFLRSGRVWRDGWGELPTSCGAYKHRATQMDAFQERVSPELGDTLFALFKTQELLDDRGVILEVHAWALDALMLKLRNLNVFSADLSGTPRQCAAVVESLLPLMSSTLSDFDSASALERAARTFNAEMG 351
               SCOP domains d1p6xb_ B: Thymidine kinase                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1p6xB00 B:21-351 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                       CATH domains
           Pfam domains (1) -----------Herpes_TK-1p6xB01 B:32-309                                                                                                                                                                                                                                                            ------------------------------------------ Pfam domains (1)
           Pfam domains (2) -----------Herpes_TK-1p6xB02 B:32-309                                                                                                                                                                                                                                                            ------------------------------------------ Pfam domains (2)
         Sec.struct. author .eeeeeeeeee.....hhhhhhhhhhhhhhh...eeee..hhhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.......eeeeee..hhhhhhhhhhhhhhh...hhhhhhhhhh........eeeeeee.hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhh............hhhhh.hhhhhhhhhh......hhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p6x B  21 HMVTIVRIYLDGVYGIGKSTTGRVMASAASGGSPTLYFPEPMAYWRTLFETDVISGIYDTQNRKQQGNLAVDDAALITAHYQSRFTTPYLILHDHTCTLFGGNSLQRGTQPDLTLVFDRHPVASTVCFPAARYLLGDMSMCALMAMVATLPREPQGGNIVVTTLNVEEHIRRLRTRARIGEQIDITLIATLRNVYFMLVNTCHFLRSGRVWRDGWGELPTSCGAYKHRATQMDAFQERVSPELGDTLFALFKTQELLDDRGVILEVHAWALDALMLKLRNLNVFSADLSGTPRQCAAVVESLLPLMSSTLSDFDSASALERAARTFNAEMG 351
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KITH_EHV4 | P24425)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0004797    thymidine kinase activity    Catalysis of the reaction: ATP + thymidine = ADP + thymidine 5'-phosphate.
    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:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006230    TMP biosynthetic process    The chemical reactions and pathways resulting in the formation of TMP, ribosylthymine monophosphate.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KITH_EHV4 | P24425: 1p72 1p73 1p75

(-) Related Entries Specified in the PDB File

1p72 EHV4-TK COMPLEXED WITH THY AND ADP
1p73 EHV4-TK COMPLEXED WITH TP4A
1p75 EHV4-TK COMPLEXED WITH TP5A
1p7c HSV1-TK COMPLEXED WITH TP5A