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(-) Description

Title :  X-RAY STRUCTURE OF CLOSTRIDIUM ACETOBUTYLICUM THYMIDINE KINASE WITH ADP. NORTHEAST STRUCTURAL GENOMICS TARGET CAR26.
 
Authors :  A. P. Kuzin, M. Abashidze, F. Forouhar, S. M. Vorobiev, T. B. Acton, L. -C R. Xiao, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Consortium (Nesg)
Date :  04 Nov 04  (Deposition) - 21 Dec 04  (Release) - 13 Jul 11  (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 :  Nesg, Northeast Structural Genomics Consortium, Protein Structure Initiative, Psi, Structural Genomics, Dna Synthesis, Kinase, Transferase, Thymidine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Kuzin, M. Abashidze, F. Forouhar, S. M. Vorobiev, T. B. Acton, L. -C. Ma, R. Xiao, G. T. Montelione, L. Tong, J. F. Hunt
X-Ray Structure Of Clostridium Acetobutylicum Thymidine Kinase With Adp. Northeast Structural Genomics Target Car26
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THYMIDINE KINASE
    Chains: A, B
    EC Number: 2.7.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: CLOSTRIDIUM ACETOBUTYLICUM
    Organism Taxid: 272562
    Strain: ATCC 824

 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  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MSE9Mod. Amino AcidSELENOMETHIONINE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MSE9Mod. Amino AcidSELENOMETHIONINE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 22)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MSE18Mod. Amino AcidSELENOMETHIONINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:145 , CYS A:148 , CYS A:183 , CYS A:186BINDING SITE FOR RESIDUE ZN A 302
2AC2SOFTWARECYS B:145 , CYS B:148 , CYS B:183 , CYS B:186BINDING SITE FOR RESIDUE ZN B 402
3AC3SOFTWARETYR A:18 , SER A:19 , GLY A:20 , LYS A:21 , SER A:22 , GLU A:23 , SER A:57 , HIS A:58 , MSE A:59 , ALA A:143 , ILE A:144 , HOH A:313 , HOH A:322 , HOH A:331 , HOH A:334 , HOH A:335 , ILE B:34BINDING SITE FOR RESIDUE ADP A 301
4AC4SOFTWAREILE A:34 , TYR B:18 , SER B:19 , GLY B:20 , LYS B:21 , SER B:22 , GLU B:23 , ALA B:143 , ILE B:144 , VAL B:146 , HOH B:405 , HOH B:424BINDING SITE FOR RESIDUE ADP B 401

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:183 -B:186

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XX6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XX6)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TK_CELLULAR_TYPEPS00603 Thymidine kinase cellular-type signature.KITH_CLOAB174-187
 		  2A:176-187
B:176-187
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TK_CELLULAR_TYPEPS00603 Thymidine kinase cellular-type signature.KITH_CLOAB174-187
 		  2A:176-187
B:176-187
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TK_CELLULAR_TYPEPS00603 Thymidine kinase cellular-type signature.KITH_CLOAB174-187
 		  4A:176-187
B:176-187

(-) Exons   (0, 0)

(no "Exon" information available for 1XX6)

(-) 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:178
 aligned with KITH_CLOAB | Q97F65 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:190
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
           KITH_CLOAB     2 YRPKDHGWVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYFEEDTEVIAIDEVQFFDDEIVEIVNKIAESGRRVICAGLDMDFRGKPFGPIPELMAIAEFVDKIQAICVVCGNPATRTQRLINGKPAFYDDPVVLIGAMESYEARCRKCHVVPQ 191
               SCOP domains d1xx6a1 A:2-142 Thymidine kinase, TK1, N-ter       minal domain                                                                              d1xx6a2 A:143-191                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.....hhhhhhhhhhhhhhhh...eeeeee.-------.eee.....eee.eee...hhhhhhh.....eeee.hhhhhhhhhhhhhhhhhhh..eeeeee...........hhhhhhhhh.eeee..ee......ee.eeeeee..ee.......-----.eeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xx6 A   2 YRPKDHGWVEVIVGPmYSGKSEELIRRIRRAKIAKQKIQVFKPE-------EDVVSHmGEKEQAVAIKNSREILKYFEEDTEVIAIDEVQFFDDEIVEIVNKIAESGRRVICAGLDmDFRGKPFGPIPELmAIAEFVDKIQAICVVCGNPATRTQRLINGKPAFYDDPV-----mESYEARCRKCHVVPQ 191
                                    11     |  21        31        41   |     - |     |61        71        81        91       101       111      |121       131|      141       151       161        |-    |  181       191
                                          17-MSE                      45      53     |                                                        118-MSE       132-MSE                               170     |               
                                                                                    59-MSE                                                                                                              176-MSE           


Chain B from PDB  Type:PROTEIN  Length:166
 aligned with KITH_CLOAB | Q97F65 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:190
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
           KITH_CLOAB     2 YRPKDHGWVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYFEEDTEVIAIDEVQFFDDEIVEIVNKIAESGRRVICAGLDMDFRGKPFGPIPELMAIAEFVDKIQAICVVCGNPATRTQRLINGKPAFYDDPVVLIGAMESYEARCRKCHVVPQ 191
               SCOP domains d1xx6b1 B:2-142 Thymidine kinase, TK1, N-ter                   minal domain                                                                  d1xx6b2 B:143-191                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------TK-1xx6B01 B:8-187                                                                                                                                                                  ---- Pfam domains (1)
           Pfam domains (2) ------TK-1xx6B02 B:8-187                                                                                                                                                                  ---- Pfam domains (2)
         Sec.struct. author .......eeeeee.....hhhhhhhhhhhhhhhh...eeeee..-------------------.ee....hhhhhhh.....eeee.hhhhhhhhhhhhhhhhhhh..eeeeee...........hhhhhhhhh.eeee..ee......ee.eeeeee..ee.......-----.eeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TK_CELLULAR_TY---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xx6 B   2 YRPKDHGWVEVIVGPmYSGKSEELIRRIRRAKIAKQKIQVFKPE-------------------AVAIKNSREILKYFEEDTEVIAIDEVQFFDDEIVEIVNKIAESGRRVICAGLDmDFRGKPFGPIPELmAIAEFVDKIQAICVVCGNPATRTQRLINGKPAFYDDPV-----mESYEARCRKCHVVPQ 191
                                    11     |  21        31        41   |     -         -   |    71        81        91       101       111      |121       131|      141       151       161        |-    |  181       191
                                          17-MSE                      45                  65                                                  118-MSE       132-MSE                               170     |               
                                                                                                                                                                                                        176-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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XX6)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KITH_CLOAB | Q97F65)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    GO:0009157    deoxyribonucleoside monophosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a deoxyribonucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with phosphate on the sugar.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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