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(-) Description

Title :  CRYSTAL STRUCTURE OF DTMP KINASE (ST1543) FROM SULFOLOBUS TOKODAII STRAIN7
 
Authors :  S. P. Kanaujia, J. Jeyakanthan, Z. A. Rafi, K. Sekar, N. Nakagawa, A. Ebi S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  20 Apr 07  (Deposition) - 22 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tmp-Binding, Atp-Binding, Thymidylate Kinase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. P. Kanaujia, J. Jeyakanthan, Z. A. Rafi, K. Sekar, N. Nakagawa, A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama
Crystal Structure Of Dtmp Kinase (St1543) From Sulfolobus Tokodaii Strain7
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE THYMIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL-21 CONDON PLUS (DE3)-RIL-X
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: SULFOLOBUS TOKODAII
    Organism Taxid: 273063
    Strain: 7
    Synonym: DTMP KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 31)

Asymmetric/Biological Unit (10, 31)
No.NameCountTypeFull Name
11PE3Ligand/IonPENTAETHYLENE GLYCOL
2CL2Ligand/IonCHLORIDE ION
3DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
4EDO6Ligand/Ion1,2-ETHANEDIOL
5EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
6MSE2Mod. Amino AcidSELENOMETHIONINE
7PEG11Ligand/IonDI(HYDROXYETHYL)ETHER
8PG41Ligand/IonTETRAETHYLENE GLYCOL
9PGE3Ligand/IonTRIETHYLENE GLYCOL
10PO41Ligand/IonPHOSPHATE ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:13 , ARG A:93 , GLN A:169BINDING SITE FOR RESIDUE CL A 214
02AC2SOFTWAREARG A:101 , TYR A:168 , HOH A:2112 , HOH A:2185BINDING SITE FOR RESIDUE CL A 215
03AC3SOFTWAREASP A:13 , GLY A:14 , SER A:15 , GLY A:16 , LYS A:17 , SER A:18 , HOH A:2049 , HOH A:2094 , HOH A:2097BINDING SITE FOR RESIDUE PO4 A 1901
04AC4SOFTWARELYS A:113 , ASP A:182 , HOH A:2003 , ILE B:109 , LEU B:159 , LYS B:178 , HOH B:1619 , HOH B:1633BINDING SITE FOR RESIDUE 1PE B 1301
05AC5SOFTWARELYS A:114 , SER A:117 , HOH A:2006 , HOH A:2023 , TRP B:111 , LYS B:114 , GLU B:174 , HOH B:1649BINDING SITE FOR RESIDUE 1PE A 1302
06AC6SOFTWAREASP B:110 , LYS B:114 , ILE B:155 , PHE B:156BINDING SITE FOR RESIDUE 1PE B 1303
07AC7SOFTWARESER A:103 , GLU A:174 , LYS A:178 , GLY B:158 , LEU B:159BINDING SITE FOR RESIDUE PGE A 1401
08AC8SOFTWAREASP A:177 , HOH A:2138 , PRO B:157BINDING SITE FOR RESIDUE PGE A 1402
09AC9SOFTWARELYS A:140 , LYS A:203 , PHE A:204 , GLU A:207 , HOH A:2200BINDING SITE FOR RESIDUE PGE A 1404
10BC1SOFTWAREGLU A:29 , LYS A:31 , ARG A:32BINDING SITE FOR RESIDUE EDO A 1501
11BC2SOFTWARESER B:117 , ALA B:119BINDING SITE FOR RESIDUE EDO B 1502
12BC3SOFTWARELYS B:55 , HOH B:1626BINDING SITE FOR RESIDUE EDO B 1503
13BC4SOFTWAREARG A:77 , HOH A:2017BINDING SITE FOR RESIDUE EDO A 1504
14BC5SOFTWARETRP A:27 , LYS A:31 , ASP A:47 , HOH A:2197BINDING SITE FOR RESIDUE EDO A 1505
15BC6SOFTWARELYS A:121 , GLU A:183 , HOH A:1982 , ARG B:129 , ASP B:177 , HOH B:1719 , HOH B:1806BINDING SITE FOR RESIDUE PG4 B 1601
16BC7SOFTWAREPRO A:60 , PHE A:63 , HIS A:67 , ASP A:102 , ARG A:105 , ASP A:154 , HOH A:2134BINDING SITE FOR RESIDUE DTT A 1701
17BC8SOFTWARETYR A:35 , THR A:37 , SER A:41 , SER A:42 , ASP A:43 , ARG A:74 , TYR A:78 , HOH A:2179BINDING SITE FOR RESIDUE EPE A 1801
18BC9SOFTWARETRP A:39 , HIS A:67 , ASP A:70 , ARG A:74 , HOH A:2037 , HOH A:2041BINDING SITE FOR RESIDUE PEG A 1201
19CC1SOFTWAREASP A:108 , TRP A:111 , HOH A:2000 , HOH A:2180 , PHE B:118BINDING SITE FOR RESIDUE PEG A 1202
20CC2SOFTWARESER A:117 , ASP B:108 , TRP B:111 , HOH B:1728 , HOH B:1733BINDING SITE FOR RESIDUE PEG B 1203
21CC3SOFTWAREGLY A:14 , ARG A:138BINDING SITE FOR RESIDUE PEG A 1204
22CC4SOFTWAREARG A:129 , ASP A:177 , HOH A:1913BINDING SITE FOR RESIDUE PEG A 1206
23CC5SOFTWAREHOH A:2131 , HOH A:2196 , HOH A:2206BINDING SITE FOR RESIDUE PEG A 1207
24CC6SOFTWAREASN A:184 , ILE A:186 , HOH A:2034 , LYS B:181 , HOH B:1709 , HOH B:1800BINDING SITE FOR RESIDUE PEG A 1208
25CC7SOFTWAREARG A:129 , SER A:131 , PRO A:132 , THR A:173 , LYS B:53 , LYS B:54 , ASP B:56BINDING SITE FOR RESIDUE PEG B 1209
26CC8SOFTWARELEU B:58 , ASP B:154BINDING SITE FOR RESIDUE PEG B 1210
27CC9SOFTWAREHOH A:2021 , LEU B:136 , LYS B:140 , GLU B:162 , GLU B:163 , LEU B:166BINDING SITE FOR RESIDUE PEG B 1211

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PLR)

(-) 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:212
 aligned with KTHY2_SULTO | Q970Q8 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  
          KTHY2_SULTO     2 KKGVLIAFEGIDGSGKSSQATLLKDWIELKRDVYLTEWNSSDWIHDIIKEAKKKDLLTPLTFSLIHATDFSDRYERYILPMLKSGFIVISDRYIYTAYARDSVRGVDIDWVKKLYSFAIKPDITFYIRVSPDIALERIKKSKRKIKPQEAGADIFPGLSPEEGFLKYQGLITEVYDKLVKDENFIVIDGTKTPKEIQIQIRKFVGELIDNSF 213
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh...hhhhhhhhh.......eeeeee.hhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2plr A   2 KKGVLIAFEGIDGSGKSSQATLLKDWIELKRDVYLTEWNSSDWIHDIIKEAKKKDLLTPLTFSLIHATDFSDRYERYILPmLKSGFIVISDRYIYTAYARDSVRGVDIDWVKKLYSFAIKPDITFYIRVSPDIALERIKKSKRKIKPQEAGADIFPGLSPEEGFLKYQGLITEVYDKLVKDENFIVIDGTKTPKEIQIQIRKFVGELIDNSF 213
                                    11        21        31        41        51        61        71        81|       91       101       111       121       131       141       151       161       171       181       191       201       211  
                                                                                                           82-MSE                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:208
 aligned with KTHY2_SULTO | Q970Q8 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:211
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212 
          KTHY2_SULTO     3 KGVLIAFEGIDGSGKSSQATLLKDWIELKRDVYLTEWNSSDWIHDIIKEAKKKDLLTPLTFSLIHATDFSDRYERYILPMLKSGFIVISDRYIYTAYARDSVRGVDIDWVKKLYSFAIKPDITFYIRVSPDIALERIKKSKRKIKPQEAGADIFPGLSPEEGFLKYQGLITEVYDKLVKDENFIVIDGTKTPKEIQIQIRKFVGELIDNSF 213
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------Thymidylate_kin-2plrB01 B:9-20   1                                                                                                                                                               ------------ Pfam domains (1)
           Pfam domains (2) ------Thymidylate_kin-2plrB02 B:9-20   1                                                                                                                                                               ------------ Pfam domains (2)
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh....eee..---hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhh...hhhhhhhhh.......eeeeee.hhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2plr B   3 KGVLIAFEGIDGSGKSSQATLLKDWIELKRDVYLTE---SDWIHDIIKEAKKKDLLTPLTFSLIHATDFSDRYERYILPmLKSGFIVISDRYIYTAYARDSVRGVDIDWVKKLYSFAIKPDITFYIRVSPDIALERIKKSKRKIKPQEAGADIFPGLSPEEGFLKYQGLITEVYDKLVKDENFIVIDGTKTPKEIQIQIRKFVGELIDNSF 213
                                    12        22        32     |  42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212 
                                                              38  42                                      82-MSE
   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 2PLR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PLR)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KTHY2_SULTO | Q970Q8)
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:0004798    thymidylate kinase activity    Catalysis of the reaction: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.
    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:0006233    dTDP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTDP, deoxyribosylthymine diphosphate (2'-deoxyribosylthymine5'-diphosphate).
    GO:0006235    dTTP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTTP, deoxyribosylthymine triphosphate.
    GO:0009165    nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
    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.

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 Related Entries

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        KTHY2_SULTO | Q970Q8: 4nzy 4rzu 4rzx 5h70

(-) Related Entries Specified in the PDB File

2pbr THE SAME PROTEIN FROM AQUIFEX AEOLICUS VF5 RELATED ID: STO001001543.1 RELATED DB: TARGETDB