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(-) Description

Title :  THIAMINE PHOSPHATE PYROPHOSPHORYLASE FROM PYROCOCCUS FURIOSUS PFU-1255191-001
 
Authors :  W. Zhou, L. Chen, W. Tempel, Z. -J. Liu, J. Habel, D. Lee, D. Lin, S. - H. Chang, B. D. Dillard, J. C. Eneh, R. C. Hopkins, F. E. Jenney Jr. , L. - L. C. Kelley, H. -S. Lee, T. Li, F. L. Poole Ii, C. Shah, F. J. Sugar, W. B. Arendall Iii, J. S. Richardson, D. C. Richardson, J. P. Rose, M. W. W. Adams, B. -C. Wang, Southeast Collaboratory For Structural Genomics (Secsg)
Date :  21 Sep 04  (Deposition) - 28 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Thiamine Phosphate Pyrophosphorylase, Southeast Collaboratory For Structural Genomics, Pyrococcus Furiosus, Hyperthermophile, Protein Structure Initiative, Psi, Secsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Zhou, L. Chen, W. Tempel, Z. -J. Liu, J. Habel, D. Lee, D. Lin, S. -H. Chang, B. D. Dillard, J. C. Eneh, R. C. Hopkins, F. E. Jenney Jr. , L. -L. C. Kelley, H. -S. Lee, T. Li, F. L. Poole Ii, C. Shah, F. J. Sugar, W. B. Arendall Iii, J. S. Richardson, D. C. Richardson, J. P. Rose, M. W. W. Adams, B. -C. Wang, Southeast Collaboratory For Structural Genomics
Thiamine Phosphate Pyrophosphorylase From Pyrococcus Furiosus Pfu-1255191-001
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIAMINE PHOSPHATE PYROPHOSPHORYLASE
    Chains: A, B
    EC Number: 2.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: THIE
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: TMP PYROPHOSPHORYLASE, TMP-PPASE, THIAMINE- PHOSPHATE SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1NI1Ligand/IonNICKEL (II) ION
2SO41Ligand/IonSULFATE ION
3UNX3Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:132 , GLY A:161 , GLY A:162 , ILE A:182 , SER A:183 , HOH A:411 , HOH A:428BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREGLU B:26 , GLU B:29BINDING SITE FOR RESIDUE NI B 302
3AC3SOFTWARESER B:183BINDING SITE FOR RESIDUE UNX B 401
4AC4SOFTWAREGLN B:36 , ARG B:38 , GLN B:83BINDING SITE FOR RESIDUE UNX B 402
5AC5SOFTWAREPRO A:19 , VAL A:21 , GLU A:22BINDING SITE FOR RESIDUE UNX A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XI3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:127 -Ser A:128
2Gly B:127 -Ser B:128

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XI3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XI3)

(-) Exons   (0, 0)

(no "Exon" information available for 1XI3)

(-) 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:202
 aligned with THIE_PYRFU | Q8U192 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      
           THIE_PYRFU     2 NLRNKLKLYVITDRRLKPEVESVREALEGGATAIQMRIKNAPTREMYEIGKTLRQLTREYDALFFVDDRVDVALAVDADGVQLGPEDMPIEVAKEIAPNLIIGASVYSLEEALEAEKKGADYLGAGSVFPTKTKEDARVIGLEGLRKIVESVKIPVVAIGGINKDNAREVLKTGVDGIAVISAVMGAEDVRKATEELRKIVEEVLG 207
               SCOP domains d1xi3a_ A: Thiamin phosphate synthase                                                                                                                                                                          SCOP domains
               CATH domains 1xi3A00 A:2-207 Aldolase class I                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.eeee......hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh..eeee.....hhhhhhhhh...eeeeee.hhhhhhhhhhhh..eeeee.....----....hhhhhhhhhhhhh...eeee......hhhhhhh....eeeehhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xi3 A   2 NLRNKLKLYVITDRRLKPEVESVREALEGGATAIQMRIKNAPTREMYEIGKTLRQLTREYDALFFVDDRVDVALAVDADGVQLGPEDMPIEVAKEIAPNLIIGASVYSLEEALEAEKKGADYLGAGSVFPT----DARVIGLEGLRKIVESVKIPVVAIGGINKDNAREVLKTGVDGIAVISAVMGAEDVRKATEELRKIVEEVLG 207
                                    11        21        31        41        51        61        71        81        91       101       111       121       131|    | 141       151       161       171       181       191       201      
                                                                                                                                                            132  137                                                                      


Chain B from PDB  Type:PROTEIN  Length:202
 aligned with THIE_PYRFU | Q8U192 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      
           THIE_PYRFU     2 NLRNKLKLYVITDRRLKPEVESVREALEGGATAIQMRIKNAPTREMYEIGKTLRQLTREYDALFFVDDRVDVALAVDADGVQLGPEDMPIEVAKEIAPNLIIGASVYSLEEALEAEKKGADYLGAGSVFPTKTKEDARVIGLEGLRKIVESVKIPVVAIGGINKDNAREVLKTGVDGIAVISAVMGAEDVRKATEELRKIVEEVLG 207
               SCOP domains d1xi3b_ B: Thiamin phosphate synthase                                                                                                                                                                          SCOP domains
               CATH domains 1xi3B00 B:2-207 Aldolase class I                                                                                                                                                                               CATH domains
           Pfam domains (1) -------TMP-TENI-1xi3B01 B:9-185                                                                                                                                                         ---------------------- Pfam domains (1)
           Pfam domains (2) -------TMP-TENI-1xi3B02 B:9-185                                                                                                                                                         ---------------------- Pfam domains (2)
         Sec.struct. author hhhhhh.eeee......hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhh...eeee.....hhhhhhhhh...eeeeee.hhhhhhhhhhhh..eeee......----....hhhhhhhhhhhhh...eeee......hhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xi3 B   2 NLRNKLKLYVITDRRLKPEVESVREALEGGATAIQMRIKNAPTREMYEIGKTLRQLTREYDALFFVDDRVDVALAVDADGVQLGPEDMPIEVAKEIAPNLIIGASVYSLEEALEAEKKGADYLGAGSVFPT----DARVIGLEGLRKIVESVKIPVVAIGGINKDNAREVLKTGVDGIAVISAVMGAEDVRKATEELRKIVEEVLG 207
                                    11        21        31        41        51        61        71        81        91       101       111       121       131|    | 141       151       161       171       181       191       201      
                                                                                                                                                            132  137
   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, 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: TIM_barrel (694)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (THIE_PYRFU | Q8U192)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    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: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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