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(-) Description

Title :  4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE PHOSPHATE KINASE FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH 4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE
 
Authors :  G. Cheng, E. M. Bennett, T. P. Begley, S. E. Ealick
Date :  07 Sep 01  (Deposition) - 27 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Thid, Ribokinase Family, Kinase, Phosphorylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Cheng, E. M. Bennett, T. P. Begley, S. E. Ealick
Crystal Structure Of 4-Amino-5-Hydroxymethyl-2-Methylpyrimidine Phosphate Kinase From Salmonella Typhimurium At 2. 3 A Resolution.
Structure V. 10 225 2002
PubMed-ID: 11839308  |  Reference-DOI: 10.1016/S0969-2126(02)00708-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOMETHYLPYRIMIDINE KINASE
    Chains: A, B
    EC Number: 2.7.4.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: THID
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Synonym: HMP-PHOSPHATE KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1HMH2Ligand/Ion4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE
2SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:105 , THR A:106 , GLU A:142 , LYS A:176 , GLY A:212 , SO4 A:2005BINDING SITE FOR RESIDUE SO4 A 2003
2AC2SOFTWAREASP B:105 , THR B:106 , GLU B:142 , LYS B:176 , GLY B:212 , SO4 B:2006BINDING SITE FOR RESIDUE SO4 B 2004
3AC3SOFTWARETHR A:208 , HIS A:209 , GLY A:210 , HMH A:2001 , SO4 A:2003BINDING SITE FOR RESIDUE SO4 A 2005
4AC4SOFTWARETHR B:208 , GLY B:210 , THR B:211 , GLY B:212 , HMH B:2002 , SO4 B:2004BINDING SITE FOR RESIDUE SO4 B 2006
5AC5SOFTWAREGLY A:11 , THR A:12 , GLU A:44 , LYS A:111 , CYS A:213 , SO4 A:2005 , HOH A:2023BINDING SITE FOR RESIDUE HMH A 2001
6AC6SOFTWAREGLY B:11 , THR B:12 , GLU B:44 , MET B:80 , CYS B:213 , SO4 B:2006 , HOH B:2014BINDING SITE FOR RESIDUE HMH B 2002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JXI)

(-) Sequences/Alignments

Asymmetric/Biological 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 THID_SALTY | P55882 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:266
                                    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       260      
           THID_SALTY     1 MQRINALTIAGTDPSGGAGIQADLKTFSALGAYGCSVITALVAQNTCGVQSVYRIEPDFVAAQLDSVFSDVRIDTTKIGMLAETDIVEAVAERLQRHHVRNVVLDTVMLAKSGDPLLSPSAIETLRVRLLPQVSLITPNLPEAAALLDAPHARTEQEMLAQGRALLAMGCEAVLMKGGHLEDAQSPDWLFTREGEQRFSAPRVNTKNTHGTGCTLSAALAALRPRHRSWGETVNEAKAWLSAALAQADTLEVGKGIGPVHHFHAWW 266
               SCOP domains d1jxia_ A: 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMP-phosphate kinase, ThiD)                                                                                                                                                                        SCOP domains
               CATH domains 1jxiA00 A:1-266  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee......hhhhhhhhhhhhh..eeeeeeeeeeeee..eeeeeee.hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhh....eeee............hhhhhhhhhhhhhhhh.eee.hhhhhhhhhh.....hhhhhhhhhhhhhhh...eeee..---------.eee....eee.---........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jxi A   1 MQRINALTIAGTDPSGGAGIQADLKTFSALGAYGCSVITALVAENTCGVQSVYRIEPDFVAAQLDSVFSDVRIDTTKIGMLAETDIVEAVAERLQRHHVRNVVLDTVMLAKSGDPLLSPSAIETLRVRLLPQVSLITPNLPEAAALLDAPHARTEQEMLAQGRALLAMGCEAVLMKG---------DWLFTREGEQRF---RVNTKNTHGTGCTLSAALAALRPRHRSWGETVNEAKAWLSAALAQADTLEVGKGIGPVHHFHAWW 266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170      |  -      |190       | - |     210       220       230       240       250       260      
                                                                                                                                                                                                          177       187        198 202                                                                


Chain B from PDB  Type:PROTEIN  Length:254
 aligned with THID_SALTY | P55882 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:266
                                    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       260      
           THID_SALTY     1 MQRINALTIAGTDPSGGAGIQADLKTFSALGAYGCSVITALVAQNTCGVQSVYRIEPDFVAAQLDSVFSDVRIDTTKIGMLAETDIVEAVAERLQRHHVRNVVLDTVMLAKSGDPLLSPSAIETLRVRLLPQVSLITPNLPEAAALLDAPHARTEQEMLAQGRALLAMGCEAVLMKGGHLEDAQSPDWLFTREGEQRFSAPRVNTKNTHGTGCTLSAALAALRPRHRSWGETVNEAKAWLSAALAQADTLEVGKGIGPVHHFHAWW 266
               SCOP domains d1jxib_ B: 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase (HMP-phosphate kinase, ThiD)                                                                                                                                                                        SCOP domains
               CATH domains 1jxiB00 B:1-266  [code=3.40.1190.20, no name defined]                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) ------------Phos_pyr_kin-1jxiB01 B:13-260                                                                                                                                                                                                                           ------ Pfam domains (1)
           Pfam domains (2) ------------Phos_pyr_kin-1jxiB02 B:13-260                                                                                                                                                                                                                           ------ Pfam domains (2)
         Sec.struct. author ....eeeeeee......hhhhhhhhhhhhh..eeeeeeeeeeeee..eeeeeee.hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhh....eeee............hhhhhhhhhhhhhhhh.eee.hhhhhhhhhh.....hhhhhhhhhhhhhhh...eeee..---------.eee....eee.---........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jxi B   1 MQRINALTIAGTDPSGGAGIQADLKTFSALGAYGCSVITALVAENTCGVQSVYRIEPDFVAAQLDSVFSDVRIDTTKIGMLAETDIVEAVAERLQRHHVRNVVLDTVMLAKSGDPLLSPSAIETLRVRLLPQVSLITPNLPEAAALLDAPHARTEQEMLAQGRALLAMGCEAVLMKG---------DWLFTREGEQRF---RVNTKNTHGTGCTLSAALAALRPRHRSWGETVNEAKAWLSAALAQADTLEVGKGIGPVHHFHAWW 266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170      |  -      |190       | - |     210       220       230       240       250       260      
                                                                                                                                                                                                          177       187        198 202
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Ribokinase (55)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (THID_SALTY | P55882)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008902    hydroxymethylpyrimidine kinase activity    Catalysis of the reaction: 4-amino-5-hydroxymethyl-2-methylpyrimidine + ATP = 4-amino-2-methyl-5-phosphomethylpyrimidine + ADP + 2 H(+).
    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.
    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.

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 Related Entries

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        THID_SALTY | P55882: 1jxh 1llj

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