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(-) Description

Title :  MOUSE THIAMIN PYROPHOSPHOKINASE IN A TERNARY COMPLEX WITH PYRITHIAMIN PYROPHOSPHATE AND AMP AT 2.5 ANGSTROM
 
Authors :  J. Y. Liu, D. E. Timm, T. D. Hurley
Date :  14 Nov 05  (Deposition) - 29 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Beta Barrel, Alpha/Beta/Alpha Sandwich, Pyrophosphokinase, Amp, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Y. Liu, D. E. Timm, T. D. Hurley
Pyrithiamine As A Substrate For Thiamine Pyrophosphokinase
J. Biol. Chem. V. 281 6601 2006
PubMed-ID: 16365036  |  Reference-DOI: 10.1074/JBC.M510951200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIAMIN PYROPHOSPHOKINASE 1
    Chains: A, B
    EC Number: 2.7.6.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: TPK1
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: THIAMINE PYROPHOSPHOKINASE 1, MTPK1

 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  (5, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MG2Ligand/IonMAGNESIUM ION
4PYI2Ligand/Ion1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-METHYLPYRIDINIUM
5SO46Ligand/IonSULFATE ION
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4PYI2Ligand/Ion1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-METHYLPYRIDINIUM
5SO46Ligand/IonSULFATE ION
Biological Unit 2 (4, 20)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4PYI4Ligand/Ion1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-METHYLPYRIDINIUM
5SO412Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:46 , ASP A:71 , ASP A:73 , ASP A:100 , AMP A:301 , PYI A:902BINDING SITE FOR RESIDUE MG A 901
02AC2SOFTWAREASP B:46 , ASP B:71 , ASP B:100 , EPE B:2201 , PYI B:2202BINDING SITE FOR RESIDUE MG B 902
03AC3SOFTWAREGLY A:58 , ARG A:60 , SO4 A:405 , HOH A:905BINDING SITE FOR RESIDUE SO4 A 401
04AC4SOFTWAREGLY B:58 , GLU B:59 , ARG B:60 , TYR B:82 , HOH B:2264BINDING SITE FOR RESIDUE SO4 B 402
05AC5SOFTWAREHIS A:98 , THR A:99 , THR A:102 , ASN A:140 , THR A:141 , GLN A:144 , PYI A:902BINDING SITE FOR RESIDUE SO4 A 403
06AC6SOFTWARELYS A:85 , LYS A:86 , SO4 A:401 , HOH A:905BINDING SITE FOR RESIDUE SO4 A 405
07AC7SOFTWARELEU A:142 , VAL A:151 , PRO A:152 , ILE A:153 , TYR A:163 , HOH A:904BINDING SITE FOR RESIDUE SO4 A 406
08AC8SOFTWARELEU B:24 , ASN B:25 , ASP B:46 , GLY B:47 , SER B:74 , THR B:99 , ASP B:100 , PHE B:101 , ALA B:137 , SER B:138 , MG B:902 , PYI B:2202BINDING SITE FOR RESIDUE EPE B 2201
09AC9SOFTWAREGLN A:96 , ASP A:97 , HIS A:98 , THR A:99 , ASP A:100 , ARG A:131 , GLN A:134 , AMP A:301 , SO4 A:403 , MG A:901 , HOH A:906 , HOH A:925 , TRP B:202 , SER B:216 , THR B:217 , SER B:218BINDING SITE FOR RESIDUE PYI A 902
10BC1SOFTWARETRP A:202 , SER A:216 , THR A:217 , SER A:218 , ASN A:219 , ASP B:71 , GLN B:96 , ASP B:97 , HIS B:98 , THR B:99 , ASP B:100 , ARG B:131 , MG B:902 , EPE B:2201BINDING SITE FOR RESIDUE PYI B 2202
11BC2SOFTWARELEU A:24 , ASN A:25 , GLN A:26 , ALA A:45 , ASP A:46 , GLY A:47 , SER A:74 , THR A:99 , ASP A:100 , PHE A:101 , GLY A:127 , GLY A:129 , GLY A:130 , ARG A:131 , GLN A:134 , MG A:901 , PYI A:902 , HOH A:942BINDING SITE FOR RESIDUE AMP A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F17)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F17)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F17)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F17)

(-) Exons   (0, 0)

(no "Exon" information available for 2F17)

(-) 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:255
 aligned with TPK1_MOUSE | Q9R0M5 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:255
                                        1                                                                                                                                                                                                                                                  
                                     -  |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238     
           TPK1_MOUSE     - ------------MEHAFTPLEPLLPTGNLKYCLVVLNQPLDARFRHLWKKALLRACADGGANHLYDLTEGERESFLPEFVSGDFDSIRPEVKEYYTKKGCDLISTPDQDHTDFTKCLQVLQRKIEEKELQVDVIVTLGGLGGRFDQIMASVNTLFQATHITPVPIIIIQKDSLIYLLQPGKHRLHVDTGMEGSWCGLIPVGQPCNQVTTTGLKWNLTNDVLGFGTLVSTSNTYDGSGLVTVETDHPLLWTMAIKS 243
               SCOP domains d2f17a2 A:-11-158 Thiamin pyrophosphokinase, catalytic domain                                                                                                             d2f17a1 A:159-243 Thiamin pyrophosphokinase, substrate-binding domain                 SCOP domains
               CATH domains -----------2f17A01     2f17A02 A:12-158 Thiamin pyrophosphokinase, domain 1                                                                                               2f17A01 A:0-11,A:159-243  [code=2.60.120.320, no name defined]                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee..hhhhh......eeeee.......hhhhhhhhh.eeeee.hhhhhhhhhh..hhhhh...eeee.....hhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhhh....eeeee..eeeeee..eeeeee.....eeeeeeee.....eeeeeee........eee......eeee......eeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f17 A -11 HHSSGLVPRGSHMEHAFTPLEPLLPTGNLKYCLVVLNQPLDARFRHLWKKALLRACADGGANHLYDLTEGERESFLPEFVSGDFDSIRPEVKEYYTKKGCDLISTPDQDHTDFTKCLQVLQRKIEEKELQVDVIVTLGGLGGRFDQIMASVNTLFQATHITPVPIIIIQKDSLIYLLQPGKHRLHVDTGMEGSWCGLIPVGQPCNQVTTTGLKWNLTNDVLGFGTLVSTSNTYDGSGLVTVETDHPLLWTMAIKS 243
                                    -2         8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238     


Chain B from PDB  Type:PROTEIN  Length:243
 aligned with TPK1_MOUSE | Q9R0M5 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           TPK1_MOUSE     1 MEHAFTPLEPLLPTGNLKYCLVVLNQPLDARFRHLWKKALLRACADGGANHLYDLTEGERESFLPEFVSGDFDSIRPEVKEYYTKKGCDLISTPDQDHTDFTKCLQVLQRKIEEKELQVDVIVTLGGLGGRFDQIMASVNTLFQATHITPVPIIIIQKDSLIYLLQPGKHRLHVDTGMEGSWCGLIPVGQPCNQVTTTGLKWNLTNDVLGFGTLVSTSNTYDGSGLVTVETDHPLLWTMAIKS 243
               SCOP domains d2f17b1 B:1-158 Thiamin pyrophosphokinase, catalytic domain                                                                                                   d2f17b2 B:159-243 Thiamin pyrophosphokinase, substrate-binding domain                 SCOP domains
               CATH domains 2f17B01    2f17B02 B:12-158 Thiamin pyrophosphokinase, domain 1                                                                                               2f17B01 B:1-11,B:159-243  [code=2.60.120.320, no name defined]                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhh......eeeee.......hhhhhhhhh.eeeee.hhhhhhhhhh..hhhhh...eeee.....hhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhhh....eeeee..eeeeee..eeeeee.....eeeeeeee.....eeeeeee........eee......eeee......eeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f17 B   1 MEHAFTPLEPLLPTGNLKYCLVVLNQPLDARFRHLWKKALLRACADGGANHLYDLTEGERESFLPEFVSGDFDSIRPEVKEYYTKKGCDLISTPDQDHTDFTKCLQVLQRKIEEKELQVDVIVTLGGLGGRFDQIMASVNTLFQATHITPVPIIIIQKDSLIYLLQPGKHRLHVDTGMEGSWCGLIPVGQPCNQVTTTGLKWNLTNDVLGFGTLVSTSNTYDGSGLVTVETDHPLLWTMAIKS 243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F17)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TPK1_MOUSE | Q9R0M5)
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:0030975    thiamine binding    Interacting selectively and non-covalently with thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
    GO:0004788    thiamine diphosphokinase activity    Catalysis of the reaction: ATP + thiamine = AMP + thiamine 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: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.
    GO:0009229    thiamine diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.
    GO:0006772    thiamine metabolic process    The chemical reactions and pathways involving thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.

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  2f17
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 Related Entries

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

UniProtKB/Swiss-Prot
        TPK1_MOUSE | Q9R0M5: 1ig3

(-) Related Entries Specified in the PDB File

1ig3 THE SAME PROTEIN COMPLEXED WITH PYRITHIAMIN PYROPHOSPHATE AND MGAMP