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(-) Description

Title :  CRYSTAL STRUCTURE OF C-TERMINAL DOMAIN OF PHOSPHOMETHYLPYRIMIDINE KINASE
 
Authors :  S. Eswaramoorthy, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  28 Mar 07  (Deposition) - 10 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Phosphate, Psi2, 10417C, Nysgxrc, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Eswaramoorthy, S. K. Burley, S. Swaminathan
Crystal Structure Of C-Terminal Domain Of Phosphomethylpyrimidine Kinase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOMETHYLPYRIMIDINE KINASE
    Atcc: 43587
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSGX3(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Gene: PF1333
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Strain: DSM 3638, JCM 8422, VC1
    Synonym: HMP-PHOSPHATE KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2PO44Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:298 , ARG A:320 , SER A:339 , ASP A:340 , HIS A:341 , LEU A:342BINDING SITE FOR RESIDUE PO4 A 500
2AC2SOFTWAREHOH B:26 , ASN B:298 , ARG B:320 , SER B:339 , ASP B:340 , HIS B:341 , LEU B:342BINDING SITE FOR RESIDUE PO4 B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PB9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:305 -Pro A:306
2Leu B:305 -Pro B:306

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PB9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PB9)

(-) Exons   (0, 0)

(no "Exon" information available for 2PB9)

(-) 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:184
 aligned with Q8U193_PYRFU | Q8U193 from UniProtKB/TrEMBL  Length:451

    Alignment length:184
                                   277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447    
         Q8U193_PYRFU   268 EKWRIYEELTNAVREFESINPVRLIPEVGTNFVYSLPLPYARSTKDVAGVKGRIVKYGNSVKAVGPVEFGASDHLARAVLTYMRFYPEYRSAINIRYSREIIEEIIEIAQERGFKVSFYDRREEPEEIKAKEGATIPWGIETAIKRIKERPDIIYHLGDVGKEPMILVFGRNPREVLEKIKMLI 451
               SCOP domains d2pb9a1 A:268-451 Phosphomethylpyrimidine kinase                                                                                                                                         SCOP domains
               CATH domains 2pb9A00 A:268-451 L-fuculose-1-phosphate Aldolase                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh............eeee.......hhh.eeee...eee....eee...eee...hhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhh..hhhhhhhhhhhhhh...eeeeee........eeeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pb9 A 268 EKWRIYEELTNAVREFESINPVRLIPEVGTNFVYSLPLPYARSTKDVAGVKGRIVKYGNSVKAVGPVEFGASDHLARAVLTYmRFYPEYRSAINIRYSREIIEEIIEIAQERGFKVSFYDRREEPEEIKAKEGATIPWGIETAIKRIKERPDIIYHLGDVGKEPmILVFGRNPREVLEKIKmLI 451
                                   277       287       297       307       317       327       337       347  |    357       367       377       387       397       407       417       427    |  437       447 |  
                                                                                                            350-MSE                                                                           432-MSE          449-MSE


Chain B from PDB  Type:PROTEIN  Length:184
 aligned with Q8U193_PYRFU | Q8U193 from UniProtKB/TrEMBL  Length:451

    Alignment length:184
                                   277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447    
         Q8U193_PYRFU   268 EKWRIYEELTNAVREFESINPVRLIPEVGTNFVYSLPLPYARSTKDVAGVKGRIVKYGNSVKAVGPVEFGASDHLARAVLTYMRFYPEYRSAINIRYSREIIEEIIEIAQERGFKVSFYDRREEPEEIKAKEGATIPWGIETAIKRIKERPDIIYHLGDVGKEPMILVFGRNPREVLEKIKMLI 451
               SCOP domains d2pb9b_ B: Phosphomethylpyrimidine kinase                                                                                                                                                SCOP domains
               CATH domains 2pb9B00 B:268-451 L-fuculose-1-phosphate Aldolase                                                                                                                                        CATH domains
           Pfam domains (1) ------Aldolase_2-2pb9B01 B:274-450                                                                                                                                                     - Pfam domains (1)
           Pfam domains (2) ------Aldolase_2-2pb9B02 B:274-450                                                                                                                                                     - Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh......eeee.......hhh.eeee...eee....eee...eee...hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhh...eee......hhhhhhh..hhhhhhhhhhhhh......eeee........eeeeee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pb9 B 268 EKWRIYEELTNAVREFESINPVRLIPEVGTNFVYSLPLPYARSTKDVAGVKGRIVKYGNSVKAVGPVEFGASDHLARAVLTYmRFYPEYRSAINIRYSREIIEEIIEIAQERGFKVSFYDRREEPEEIKAKEGATIPWGIETAIKRIKERPDIIYHLGDVGKEPmILVFGRNPREVLEKIKmLI 451
                                   277       287       297       307       317       327       337       347  |    357       367       377       387       397       407       417       427    |  437       447 |  
                                                                                                            350-MSE                                                                           432-MSE          449-MSE
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Ribokinase (55)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8U193_PYRFU | Q8U193)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0008972    phosphomethylpyrimidine kinase activity    Catalysis of the reaction: ATP + 4-amino-2-methyl-5-phosphomethylpyrimidine = ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine.
    GO:0004789    thiamine-phosphate diphosphorylase activity    Catalysis of the reaction: 4-amino-2-methyl-5-diphosphomethylpyrimidine + 4-methyl-5-(2-phosphoethyl)-thiazole + H(+) = diphosphate + thiamine phosphate.
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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