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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF PHOSPHOMETHYLPYRIMIDINE KINASE (THID) FROM THERMUS THERMOPHILUS HB8
 
Authors :  B. Bagautdinov, S. Kuramitsu, S. Yokoyama, M. Miyano, T. H. Tahirov, Ri Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 Mar 03  (Deposition) - 08 Apr 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Thiamin Biosynthesis, Thid, Ribokinase Family, Phosphorylation, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Bagautdinov, S. Kuramitsu, S. Yokoyama, M. Miyano, T. H. Tahirov
Crystal Structure Analysis Of Phosphomethylpyrimidine Kinas (Thid) From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHOMETHYLPYRIMIDINE KINASE
    Chains: A
    EC Number: 2.7.4.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: THID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Synonym: THID

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1DIO2Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GOL4Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1DIO4Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GOL8Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:27 , PHE A:28 , ARG A:239 , ALA A:258 , HOH A:562BINDING SITE FOR RESIDUE SO4 A 400
2AC2SOFTWAREMET A:1 , GLY A:29 , TRP A:257BINDING SITE FOR RESIDUE DIO A 500
3AC3SOFTWAREGLU A:56 , GLU A:90BINDING SITE FOR RESIDUE DIO A 502
4AC4SOFTWARELEU A:52 , LEU A:53 , ASP A:81 , ALA A:83 , HOH A:527 , HOH A:568BINDING SITE FOR RESIDUE GOL A 300
5AC5SOFTWAREARG A:94BINDING SITE FOR RESIDUE GOL A 301
6AC6SOFTWAREPRO A:99 , LEU A:220 , ARG A:224BINDING SITE FOR RESIDUE GOL A 302
7AC7SOFTWAREHOH A:505BINDING SITE FOR RESIDUE GOL A 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UB0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:98 -Pro A:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UB0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UB0)

(-) Exons   (0, 0)

(no "Exon" information available for 1UB0)

(-) 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:246
 aligned with Q7SIA0_THETH | Q7SIA0 from UniProtKB/TrEMBL  Length:258

    Alignment length:258
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250        
         Q7SIA0_THETH     1 MRVALTIAGSDSGGGAGVQADLKVFFRFGVYGTSALTLVTAQNTLGVQRVHLLPPEVVYAQIESVAQDFPLHAAKTGALGDAAIVEAVAEAVRRFGVRPLVVDPVMVAKSGDPLLAKEAAAALKERLFPLADLVTPNRLEAEALLGRPIRTLKEAEEAAKALLALGPKAVLLKGGHLEGEEAVDLLATRGGVLRFSAPRVHTRNTHGTGCTLSAAIAALLAKGRPLAEAVAEAKAYLTRALKTAPSLGHGHGPLDHWA 258
               SCOP domains d1ub0a_ A: 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMP-phosphate kinase, ThiD)                                                                                                                                                                SCOP domains
               CATH domains 1ub0A00 A:1-258  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                              CATH domains
               Pfam domains ----------Phos_pyr_kin-1ub0A01 A:11-255                                                                                                                                                                                                                        --- Pfam domains
         Sec.struct. author ..eeeeeeeee....hhhhhhhhhhhhh..eeeeeeeeeeeee..eeeeeee.hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh....eee....---------hhhhhhhhhhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhh.....eeeeeee.---.eeeeeee..eeeeeee.........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ub0 A   1 MRVALTIAGSDSGGGAGVQADLKVFFRFGVYGTSALTLVTAQNTLGVQRVHLLPPEVVYAQIESVAQDFPLHAAKTGALGDAAIVEAVAEAVRRFGVRPLVVDPVM---------AKEAAAALKERLFPLADLVTPNRLEAEALLGRPIRTLKEAEEAAKALLALGPKAVLLKGGHL---EAVDLLATRGGVLRFSAPRVHTRNTHGTGCTLSAAIAALLAKGRPLAEAVAEAKAYLTRALKTAPSLGHGHGPLDHWA 258
                                    10        20        30        40        50        60        70        80        90       100     |   -     | 120       130       140       150       160       170      |  -|      190       200       210       220       230       240       250        
                                                                                                                                   106       116                                                          177 181
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Ribokinase (55)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q7SIA0_THETH | Q7SIA0)
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:0008972    phosphomethylpyrimidine kinase activity    Catalysis of the reaction: ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine = ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine.
    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:0009228    thiamine biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.

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