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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST THYMIDYLATE KINASE COMPLEXED WITH THE BISUBSTRATE INHIBITOR TP5A AT 2.0 A RESOLUTION: IMPLICATIONS FOR CATALYSIS AND AZT ACTIVATION
 
Authors :  A. Lavie, I. Schlichting, M. Konrad, R. S. Goody, R. Brundiers, J. Reinstein
Date :  26 Jan 98  (Deposition) - 16 Feb 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Kinase, Phosphotransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Lavie, M. Konrad, R. Brundiers, R. S. Goody, I. Schlichting, J. Reinstein
Crystal Structure Of Yeast Thymidylate Kinase Complexed With The Bisubstrate Inhibitor P1-(5'-Adenosyl) P5-(5'-Thymidyl) Pentaphosphate (Tp5A) At 2. 0 A Resolution: Implications For Catalysis And Azt Activation.
Biochemistry V. 37 3677 1998
PubMed-ID: 9521686  |  Reference-DOI: 10.1021/BI9720787
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THYMIDYLATE KINASE
    ChainsA, B, C, D, E, F, G, H
    EC Number2.7.4.9
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)AB      
Biological Unit 2 (1x)  CD    
Biological Unit 3 (1x)    EF  
Biological Unit 4 (1x)      GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1T5A8Ligand/IonP1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1T5A2Ligand/IonP1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1T5A2Ligand/IonP1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1T5A2Ligand/IonP1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1T5A2Ligand/IonP1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:14 , ARG A:15 , THR A:16 , GLY A:17 , LYS A:18 , THR A:19 , THR A:20 , LYS A:37 , PHE A:38 , PRO A:39 , ARG A:41 , LEU A:53 , PHE A:69 , ARG A:73 , ARG A:94 , GLY A:99 , TYR A:102 , GLU A:142 , LYS A:143 , SER A:144 , GLU A:149 , TYR A:151 , LYS A:187 , GLY A:188 , ILE A:189 , HOH A:4063 , HOH A:4064 , HOH A:4067 , HOH A:4069 , HOH A:4070 , HOH A:4071 , HOH A:4084 , HOH A:4438 , HOH A:4454 , HOH A:4499 , HOH A:4554BINDING SITE FOR RESIDUE T5A A 217
2AC2SOFTWAREASP B:14 , ARG B:15 , THR B:16 , GLY B:17 , LYS B:18 , THR B:19 , THR B:20 , LYS B:37 , PHE B:38 , PRO B:39 , ARG B:41 , PHE B:69 , ARG B:73 , ARG B:94 , GLY B:99 , TYR B:102 , LYS B:143 , GLU B:149 , TYR B:151 , LYS B:187 , GLY B:188 , ILE B:189 , HOH B:4010 , HOH B:4011 , HOH B:4014 , HOH B:4016 , HOH B:4017 , HOH B:4018 , HOH B:4055 , HOH B:4538 , HOH B:4578 , HOH B:4579 , HOH B:4725 , HOH B:4935BINDING SITE FOR RESIDUE T5A B 217
3AC3SOFTWAREASP C:14 , ARG C:15 , THR C:16 , GLY C:17 , LYS C:18 , THR C:19 , THR C:20 , LYS C:37 , PHE C:38 , PRO C:39 , ARG C:41 , PHE C:69 , ARG C:73 , ARG C:94 , SER C:98 , GLY C:99 , TYR C:102 , TYR C:151 , LYS C:187 , GLY C:188 , ILE C:189 , HOH C:4173 , HOH C:4174 , HOH C:4177 , HOH C:4180 , HOH C:4181 , HOH C:4561 , HOH C:4946BINDING SITE FOR RESIDUE T5A C 217
4AC4SOFTWAREASP D:14 , ARG D:15 , THR D:16 , GLY D:17 , LYS D:18 , THR D:19 , THR D:20 , LYS D:37 , PHE D:38 , ARG D:41 , PHE D:69 , ARG D:73 , ARG D:94 , GLY D:99 , TYR D:102 , LYS D:143 , GLU D:149 , TYR D:151 , LYS D:187 , GLY D:188 , ILE D:189 , HOH D:4122 , HOH D:4123 , HOH D:4126 , HOH D:4127 , HOH D:4128 , HOH D:4129 , HOH D:4167 , HOH D:4191 , HOH D:4221 , HOH D:5317BINDING SITE FOR RESIDUE T5A D 217
5AC5SOFTWAREASP E:14 , ARG E:15 , THR E:16 , GLY E:17 , LYS E:18 , THR E:19 , THR E:20 , LYS E:37 , PHE E:38 , PRO E:39 , ARG E:41 , LEU E:53 , PHE E:69 , ARG E:73 , ARG E:94 , GLY E:99 , TYR E:102 , GLU E:142 , SER E:144 , GLU E:149 , TYR E:151 , LYS E:187 , GLY E:188 , ILE E:189 , HOH E:4287 , HOH E:4288 , HOH E:4291 , HOH E:4296 , HOH E:4297 , HOH E:4307 , HOH E:4938 , HOH E:5329 , HOH E:5347 , HOH E:5354BINDING SITE FOR RESIDUE T5A E 217
6AC6SOFTWAREASP F:14 , ARG F:15 , THR F:16 , GLY F:17 , LYS F:18 , THR F:19 , THR F:20 , LYS F:37 , PHE F:38 , PRO F:39 , ARG F:41 , LEU F:53 , PHE F:69 , ARG F:73 , ARG F:94 , GLY F:99 , TYR F:102 , LYS F:143 , GLU F:149 , TYR F:151 , LYS F:187 , GLY F:188 , ILE F:189 , HOH F:4237 , HOH F:4238 , HOH F:4241 , HOH F:4242 , HOH F:4244 , HOH F:4281 , HOH F:4836 , HOH F:4841 , HOH F:5082 , HOH F:5127 , HOH F:5136BINDING SITE FOR RESIDUE T5A F 217
7AC7SOFTWAREASP G:14 , ARG G:15 , THR G:16 , GLY G:17 , LYS G:18 , THR G:19 , THR G:20 , LYS G:37 , PHE G:38 , PRO G:39 , ARG G:41 , LEU G:53 , PHE G:69 , ARG G:73 , ARG G:94 , GLY G:99 , TYR G:102 , GLU G:142 , LYS G:143 , SER G:144 , GLU G:149 , TYR G:151 , LYS G:187 , GLY G:188 , ILE G:189 , HOH G:4404 , HOH G:4405 , HOH G:4409 , HOH G:4412 , HOH G:4413 , HOH G:4414 , HOH G:4532 , HOH G:4535 , HOH G:4585 , HOH G:4643 , HOH G:4928BINDING SITE FOR RESIDUE T5A G 217
8AC8SOFTWAREASP H:14 , ARG H:15 , THR H:16 , GLY H:17 , LYS H:18 , THR H:19 , THR H:20 , LYS H:37 , PHE H:38 , PRO H:39 , ARG H:41 , LEU H:53 , PHE H:69 , ARG H:73 , ARG H:94 , GLY H:99 , TYR H:102 , GLU H:149 , TYR H:151 , LYS H:187 , GLY H:188 , ILE H:189 , HOH H:4347 , HOH H:4348 , HOH H:4351 , HOH H:4353 , HOH H:4354 , HOH H:4355 , HOH H:4397 , HOH H:4503 , HOH H:4608 , HOH H:4803 , HOH H:4808 , HOH H:5010BINDING SITE FOR RESIDUE T5A H 217

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TMK)

(-) Cis Peptide Bonds  (16, 16)

Asymmetric Unit
No.Residues
1Gln A:30 -Pro A:31
2Phe A:38 -Pro A:39
3Gln B:30 -Pro B:31
4Phe B:38 -Pro B:39
5Gln C:30 -Pro C:31
6Phe C:38 -Pro C:39
7Gln D:30 -Pro D:31
8Phe D:38 -Pro D:39
9Gln E:30 -Pro E:31
10Phe E:38 -Pro E:39
11Gln F:30 -Pro F:31
12Phe F:38 -Pro F:39
13Gln G:30 -Pro G:31
14Phe G:38 -Pro G:39
15Gln H:30 -Pro H:31
16Phe H:38 -Pro H:39

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TMK)

(-) PROSITE Motifs  (1, 8)

Asymmetric Unit (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_KINASEPS01331 Thymidylate kinase signature.KTHY_YEAST91-103
 
 
 
 
 
 
 
  8A:91-103
B:91-103
C:91-103
D:91-103
E:91-103
F:91-103
G:91-103
H:91-103
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_KINASEPS01331 Thymidylate kinase signature.KTHY_YEAST91-103
 
 
 
 
 
 
 
  2A:91-103
B:91-103
-
-
-
-
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_KINASEPS01331 Thymidylate kinase signature.KTHY_YEAST91-103
 
 
 
 
 
 
 
  2-
-
C:91-103
D:91-103
-
-
-
-
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_KINASEPS01331 Thymidylate kinase signature.KTHY_YEAST91-103
 
 
 
 
 
 
 
  2-
-
-
-
E:91-103
F:91-103
-
-
Biological Unit 4 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_KINASEPS01331 Thymidylate kinase signature.KTHY_YEAST91-103
 
 
 
 
 
 
 
  2-
-
-
-
-
-
G:91-103
H:91-103

(-) Exons   (1, 8)

Asymmetric Unit (1, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YJR057W1YJR057W.1X:544054-544704651KTHY_YEAST1-2162168A:1-216
B:1-216
C:1-216 (gaps)
D:3-216
E:2-216
F:1-216
G:2-216
H:3-216
216
216
216
214
215
216
215
214

(-) 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:216
 aligned with KTHY_YEAST | P00572 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
           KTHY_YEAST     1 MMGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
               SCOP domains d3tmka_ A: Thymidylate kinase                                                                                                                                                                                            SCOP domains
               CATH domains 3tmkA00 A:1-216 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeee.....hhhhhhhhhhhh...eeeee......hhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhh..eeeee..hhhhhhhhhhh......hhhhhhhh.......eeeeee......hhh...........hhhhhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------THYMIDYLATE_K----------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-216 UniProt: 1-216                                                                                                                                                                                    Transcript 1
                 3tmk A   1 MMGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with KTHY_YEAST | P00572 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
           KTHY_YEAST     1 MMGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
               SCOP domains d3tmkb_ B: Thymidylate kinase                                                                                                                                                                                            SCOP domains
               CATH domains 3tmkB00 B:1-216 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeee.....hhhhhhhhhhhh...eeeee......hhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhh..eeeee..hhhhhhhhhhh......hhhhhhhh.......eeeeee...hhhhhh...........hhhhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhh...hhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------THYMIDYLATE_K----------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-216 UniProt: 1-216                                                                                                                                                                                    Transcript 1
                 3tmk B   1 MMGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      

Chain C from PDB  Type:PROTEIN  Length:205
 aligned with KTHY_YEAST | P00572 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
           KTHY_YEAST     1 MMGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
               SCOP domains d3tmkc_ C: Thymidylate kinase                                                                                                                                                                                            SCOP domains
               CATH domains 3tmkC00 C:1-216 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeee.....hhhhhhhhhhhh...eeeee......hhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhh..eeeee..hhhhhhhhhhh......hhhhhhhh.......eeeeee...-----------......hhhhhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------THYMIDYLATE_K----------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:1-216 (gaps) UniProt: 1-216                                                                                                                                                                             Transcript 1
                 3tmk C   1 MMGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQD-----------DERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     |   -       150       160       170       180       190       200       210      
                                                                                                                                                                 136         148                                                                    

Chain D from PDB  Type:PROTEIN  Length:214
 aligned with KTHY_YEAST | P00572 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:214
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212    
           KTHY_YEAST     3 GRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
               SCOP domains d3tmkd_ D: Thymidylate kinase                                                                                                                                                                                          SCOP domains
               CATH domains 3tmkD00 D:3-216 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhh...eeeee......hhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhh..eeeee..hhhhhhhhhhh......hhhhhhhh.......eeeeee...hhhhhh...........hhhhhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------THYMIDYLATE_K----------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:3-216 UniProt: 1-216 [INCOMPLETE]                                                                                                                                                                     Transcript 1
                 3tmk D   3 GRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212    

Chain E from PDB  Type:PROTEIN  Length:215
 aligned with KTHY_YEAST | P00572 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
           KTHY_YEAST     2 MGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
               SCOP domains d3tmke_ E: Thymidylate kinase                                                                                                                                                                                           SCOP domains
               CATH domains 3tmkE00 E:2-216 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.....hhhhhhhhhhhh...eeeee......hhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhh..eeeee..hhhhhhhhhhh......hhhhhhhh.......eeeeee......hhh...........hhhhhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------THYMIDYLATE_K----------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: E:2-216 UniProt: 1-216 [INCOMPLETE]                                                                                                                                                                      Transcript 1
                 3tmk E   2 MGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     

Chain F from PDB  Type:PROTEIN  Length:216
 aligned with KTHY_YEAST | P00572 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
           KTHY_YEAST     1 MMGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
               SCOP domains d3tmkf_ F: Thymidylate kinase                                                                                                                                                                                            SCOP domains
               CATH domains 3tmkF00 F:1-216 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeee.....hhhhhhhhhhhh...eeeee......hhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhh..eeeee..hhhhhhhhhhh......hhhhhhhh.......eeeeee...hhhhhh...........hhhhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------THYMIDYLATE_K----------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: F:1-216 UniProt: 1-216                                                                                                                                                                                    Transcript 1
                 3tmk F   1 MMGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      

Chain G from PDB  Type:PROTEIN  Length:215
 aligned with KTHY_YEAST | P00572 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
           KTHY_YEAST     2 MGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
               SCOP domains d3tmkg_ G: Thymidylate kinase                                                                                                                                                                                           SCOP domains
               CATH domains 3tmkG00 G:2-216 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.....hhhhhhhhhhhh...eeeee......hhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhh..eeeee..hhhhhhhhhhh......hhhhhhhh.......eeeeee....................hhhhhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------THYMIDYLATE_K----------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: G:2-216 UniProt: 1-216 [INCOMPLETE]                                                                                                                                                                      Transcript 1
                 3tmk G   2 MGRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     

Chain H from PDB  Type:PROTEIN  Length:214
 aligned with KTHY_YEAST | P00572 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:214
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212    
           KTHY_YEAST     3 GRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
               SCOP domains d3tmkh_ H: Thymidylate kinase                                                                                                                                                                                          SCOP domains
               CATH domains 3tmkH00 H:3-216 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                   CATH domains
           Pfam domains (1) -------Thymidylate_kin-3tmkH01 H:10-196                                                                                                                                                           -------------------- Pfam domains (1)
           Pfam domains (2) -------Thymidylate_kin-3tmkH02 H:10-196                                                                                                                                                           -------------------- Pfam domains (2)
           Pfam domains (3) -------Thymidylate_kin-3tmkH03 H:10-196                                                                                                                                                           -------------------- Pfam domains (3)
           Pfam domains (4) -------Thymidylate_kin-3tmkH04 H:10-196                                                                                                                                                           -------------------- Pfam domains (4)
           Pfam domains (5) -------Thymidylate_kin-3tmkH05 H:10-196                                                                                                                                                           -------------------- Pfam domains (5)
           Pfam domains (6) -------Thymidylate_kin-3tmkH06 H:10-196                                                                                                                                                           -------------------- Pfam domains (6)
           Pfam domains (7) -------Thymidylate_kin-3tmkH07 H:10-196                                                                                                                                                           -------------------- Pfam domains (7)
           Pfam domains (8) -------Thymidylate_kin-3tmkH08 H:10-196                                                                                                                                                           -------------------- Pfam domains (8)
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhh...eeeee......hhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhh..eeeee..hhhhhhhhhhh......hhhhhhhh.......eeeeee...hhhh.............hhhhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------THYMIDYLATE_K----------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: H:3-216 UniProt: 1-216 [INCOMPLETE]                                                                                                                                                                     Transcript 1
                 3tmk H   3 GRGKLILIEGLDRTGKTTQCNILYKKLQPNCKLLKFPERSTRIGGLINEYLTDDSFQLSDQAIHLLFSANRWEIVDKIKKDLLEGKNIVMDRYVYSGVAYSAAKGTNGMDLDWCLQPDVGLLKPDLTLFLSTQDVDNNAEKSGFGDERYETVKFQEKVKQTFMKLLDKEIRKGDESITIVDVTNKGIQEVEALIWQIVEPVLSTHIDHDKFSFF 216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212    

   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, 8)

Asymmetric Unit

(-) CATH Domains  (1, 8)

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

(-) Pfam Domains  (1, 8)

Asymmetric Unit

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (KTHY_YEAST | P00572)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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.
    GO:0009041    uridylate kinase activity    Catalysis of the reaction: ATP + (d)UMP = ADP + (d)UDP.
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:0006227    dUDP biosynthetic process    The chemical reactions and pathways resulting in the formation of dUDP, deoxyuridine diphosphate (2'-deoxy-5'-uridylyl phosphate).
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KTHY_YEAST | P005721tmk 2tmk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3TMK)