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(-) Description

Title :  MOUSE THIAMIN PYROPHOSPHOKINASE COMPLEXED WITH THIAMIN
 
Authors :  D. E. Timm, J. Liu, L. -J. Baker, R. A. Harris
Date :  16 Apr 01  (Deposition) - 25 Apr 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (2x),B (2x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Beta Barrel, Alpha/Beta/Alpha Sandwich, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. E. Timm, J. Liu, L. J. Baker, R. A. Harris
Crystal Structure Of Thiamin Pyrophosphokinase.
J. Mol. Biol. V. 310 195 2001
PubMed-ID: 11419946  |  Reference-DOI: 10.1006/JMBI.2001.4727
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIAMIN PYROPHOSPHOKINASE
    Chains: A, B
    EC Number: 2.7.6.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): A (2x)B (2x)
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1SO414Ligand/IonSULFATE ION
2VIB2Ligand/Ion3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1SO414Ligand/IonSULFATE ION
2VIB2Ligand/Ion3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM
Biological Unit 2 (2, 20)
No.NameCountTypeFull Name
1SO418Ligand/IonSULFATE ION
2VIB2Ligand/Ion3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM
Biological Unit 3 (2, 32)
No.NameCountTypeFull Name
1SO428Ligand/IonSULFATE ION
2VIB4Ligand/Ion3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:78 , GLU A:79 , ARG A:80 , HOH A:691BINDING SITE FOR RESIDUE SO4 A 602
02AC2SOFTWARELYS A:105 , LYS A:106 , HOH A:753BINDING SITE FOR RESIDUE SO4 A 603
03AC3SOFTWAREASP A:117 , HIS A:118 , THR A:119 , THR A:122 , ASN A:160 , GLN A:164 , HOH A:650BINDING SITE FOR RESIDUE SO4 A 604
04AC4SOFTWAREASN A:45 , HOH A:668 , HOH A:745BINDING SITE FOR RESIDUE SO4 A 605
05AC5SOFTWAREGLY B:78 , GLU B:79 , ARG B:80 , TYR B:102 , HOH B:761 , HOH B:809BINDING SITE FOR RESIDUE SO4 B 606
06AC6SOFTWAREHIS B:118 , THR B:119 , THR B:122 , ASN B:160 , THR B:161 , GLN B:164 , HOH B:617 , HOH B:698 , HOH B:786BINDING SITE FOR RESIDUE SO4 B 607
07AC7SOFTWAREASN B:45 , HOH B:635 , HOH B:677 , HOH B:708BINDING SITE FOR RESIDUE SO4 B 608
08AC8SOFTWARESER A:238 , VIB A:502 , ARG B:151BINDING SITE FOR RESIDUE SO4 A 609
09AC9SOFTWAREARG A:151 , HOH A:752 , SER B:238 , VIB B:501BINDING SITE FOR RESIDUE SO4 A 610
10BC1SOFTWAREGLY B:200 , SER B:201 , LYS B:262 , SER B:263 , HOH B:644BINDING SITE FOR RESIDUE SO4 B 611
11BC2SOFTWAREGLY A:200 , SER A:201 , LYS A:262 , SER A:263 , HOH A:623BINDING SITE FOR RESIDUE SO4 A 612
12BC3SOFTWAREGLN A:46 , GLY A:150 , HOH A:648 , HOH A:713 , HOH A:715 , HOH A:729 , HOH A:772BINDING SITE FOR RESIDUE SO4 A 613
13BC4SOFTWAREALA B:24 , ARG B:191 , HIS B:193 , HOH B:781BINDING SITE FOR RESIDUE SO4 B 615
14BC5SOFTWAREASN A:213 , HIS A:253 , HOH A:676 , HOH A:747 , HOH A:756 , PRO B:33 , GLY B:35 , LYS B:58BINDING SITE FOR RESIDUE SO4 A 616
15BC6SOFTWAREGLN A:116 , ASP A:117 , SO4 A:610 , TRP B:222 , SER B:236 , THR B:237 , SER B:238 , ASN B:239 , HOH B:616BINDING SITE FOR RESIDUE VIB B 501
16BC7SOFTWARETRP A:222 , SER A:236 , THR A:237 , SER A:238 , ASN A:239 , SO4 A:609 , HOH A:631 , HOH A:644 , GLN B:116 , ASP B:117 , HIS B:118 , HOH B:786BINDING SITE FOR RESIDUE VIB A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IG3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IG3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IG3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IG3)

(-) Exons   (0, 0)

(no "Exon" information available for 1IG3)

(-) 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:254
 aligned with TPK1_MOUSE | Q9R0M5 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:254
                                       1                                                                                                                                                                                                                                                  
                                     - |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239    
           TPK1_MOUSE     - -----------MEHAFTPLEPLLPTGNLKYCLVVLNQPLDARFRHLWKKALLRACADGGANHLYDLTEGERESFLPEFVSGDFDSIRPEVKEYYTKKGCDLISTPDQDHTDFTKCLQVLQRKIEEKELQVDVIVTLGGLGGRFDQIMASVNTLFQATHITPVPIIIIQKDSLIYLLQPGKHRLHVDTGMEGSWCGLIPVGQPCNQVTTTGLKWNLTNDVLGFGTLVSTSNTYDGSGLVTVETDHPLLWTMAIKS 243
               SCOP domains d1ig3a2 A:10-178 Thiamin pyrophosphokinase, catalytic domain                                                                                                             d1ig3a1 A:179-263 Thiamin pyrophosphokinase, substrate-binding domain                 SCOP domains
               CATH domains ----------1ig3A01     1ig3A02 A:32-178 Thiamin pyrophosphokinase, domain 1                                                                                               1ig3A01 A:20-31,A:179-263  [code=2.60.120.320, no name defined]                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eee..hhhhh......eeeee.......hhhhhhhhh.eeeee.hhhhhhhhh...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
                 1ig3 A  10 HSSGLVPRGSHMEHAFTPLEPLLPTGNLKYCLVVLNQPLDARFRHLWKKALLRACADGGANHLYDLTEGERESFLPEFVSGDFDSIRPEVKEYYTKKGCDLISTPDQDHTDFTKCLQVLQRKIEEKELQVDVIVTLGGLGGRFDQIMASVNTLFQATHITPVPIIIIQKDSLIYLLQPGKHRLHVDTGMEGSWCGLIPVGQPCNQVTTTGLKWNLTNDVLGFGTLVSTSNTYDGSGLVTVETDHPLLWTMAIKS 263
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259    


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 d1ig3b2 B:21-178 Thiamin pyrophosphokinase, catalytic domain                                                                                                  d1ig3b1 B:179-263 Thiamin pyrophosphokinase, substrate-binding domain                 SCOP domains
               CATH domains 1ig3B01    1ig3B02 B:32-178 Thiamin pyrophosphokinase, domain 1                                                                                               1ig3B01 B:21-31,B:179-263  [code=2.60.120.320, no name defined]                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhh......eeeee.......hhhhhhhhh.eeeee.hhhhhhhhhh..hhhhh...eeeehhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhhhh...eeeee..eeeeee..eeeeee.....eeeeeeee.....eeeeeee........eee......eeee......eeeeee...eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ig3 B  21 MEHAFTPLEPLLPTGNLKYCLVVLNQPLDARFRHLWKKALLRACADGGANHLYDLTEGERESFLPEFVSGDFDSIRPEVKEYYTKKGCDLISTPDQDHTDFTKCLQVLQRKIEEKELQVDVIVTLGGLGGRFDQIMASVNTLFQATHITPVPIIIIQKDSLIYLLQPGKHRLHVDTGMEGSWCGLIPVGQPCNQVTTTGLKWNLTNDVLGFGTLVSTSNTYDGSGLVTVETDHPLLWTMAIKS 263
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
   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 1IG3)

(-) 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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  1ig3
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 Related Entries

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        TPK1_MOUSE | Q9R0M5: 2f17

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