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(-) Description

Title :  CRYSTAL STRUCTURE OF TENA HOMOLOGUE (HP1287) FROM HELICOBACTER PYLORI
 
Authors :  N. Barison, L. Cendron, A. Trento, A. Angelini, G. Zanotti
Date :  21 Sep 07  (Deposition) - 30 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,D
Biol. Unit 1:  A,D  (2x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  D  (2x)
Keywords :  Tena, Hp1287, Helicobacter Pylori, Thiamin, Vitamin B1, Thiaminase Ii, Transcription, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Barison, L. Cendron, A. Trento, A. Angelini, G. Zanotti
The Structural And Functional Characterization Of Hp1287 From Helicobacter Pylori Demonstrates It Is A Tena Homologue
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR
    Chains: A, D
    EC Number: 3.5.99.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET151 DIRECTIONAL TOPO
    Expression System Strain: BL21-DE3
    Expression System Vector Type: PLASMID
    Gene: HP1287
    Organism Common: CAMPYLOBACTER PYLORI
    Organism Scientific: HELICOBACTER PYLORI
    Strain: CCUG17874
    Synonym: TENA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AD
Biological Unit 1 (2x): AD
Biological Unit 2 (2x): A 
Biological Unit 3 (2x):  D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2RD3)

(-) Sites  (0, 0)

(no "Site" information available for 2RD3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RD3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:149 -Pro A:150
2Ile D:149 -Pro D:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RD3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RD3)

(-) Exons   (0, 0)

(no "Exon" information available for 2RD3)

(-) 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:221
 aligned with O25874_HELPY | O25874 from UniProtKB/TrEMBL  Length:217

    Alignment length:221
                                1                                                                                                                                                                                                                        
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216 
         O25874_HELPY     - ----MQVSQYLYQNVQSIWGDCISHPFVQGIGRGTLERDKFRFYIIQDYLFLLEYAKVFALGVVKACDEAVMREFSNAIQDILNNEMSIHNHYIRGLQITQKELQNARPTLANKSYTSYMLAEGFKGSIKEVAAAVLSCGWSYLVIAQNLSQIPNALEHAFYGHWIKGYSSKEFQACVNWNINLLDSLTLTSSKQEIEKLKDIFITTSEYEYLFWDMAYQS 217
               SCOP domains d2rd3a_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rd3 A  -3 DPFTMQVSQYLYQNAQSIWGDCISHPFVQGIGRGTLERDKFRFYIIQDYLFLLEYAKVFALGVVKACDEAVMREFSNAIQDILNNEMSIHNHYIRELQITQKELQNACPTLANKSYTSYMLAEGFKGSIKEVAAAVLSCGWSYLVIAQNLSQIPNALEHAFYGHWIKGYSSKEFQACVNWNINLLDSLTLASSKQEIEKLKEIFITTSEYEYLFWDMAYQS 217
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216 


Chain A from PDB  Type:PROTEIN  Length:221
 aligned with TENA_HELPX | A8KRL3 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:221
                                1                                                                                                                                                                                                                        
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216 
           TENA_HELPX     - ----MQVSQYLYQNAQSIWGDCISHPFVQGIGRGTLERDKFRFYIIQDYLFLLEYAKVFALGVVKACDEAVMREFSNAIQDILNNEMSIHNHYIRELQITQKELQNACPTLANKSYTSYMLAEGFKGSIKEVAAAVLSCGWSYLVIAQNLSQIPNALEHAFYGHWIKGYSSKEFQACVNWNINLLDSLTLASSKQEIEKLKEIFITTSEYEYLFWDMAYQS 217
               SCOP domains d2rd3a_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rd3 A  -3 DPFTMQVSQYLYQNAQSIWGDCISHPFVQGIGRGTLERDKFRFYIIQDYLFLLEYAKVFALGVVKACDEAVMREFSNAIQDILNNEMSIHNHYIRELQITQKELQNACPTLANKSYTSYMLAEGFKGSIKEVAAAVLSCGWSYLVIAQNLSQIPNALEHAFYGHWIKGYSSKEFQACVNWNINLLDSLTLASSKQEIEKLKEIFITTSEYEYLFWDMAYQS 217
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216 


Chain D from PDB  Type:PROTEIN  Length:218
 aligned with O25874_HELPY | O25874 from UniProtKB/TrEMBL  Length:217

    Alignment length:218
                             1                                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209        
         O25874_HELPY     - -MQVSQYLYQNVQSIWGDCISHPFVQGIGRGTLERDKFRFYIIQDYLFLLEYAKVFALGVVKACDEAVMREFSNAIQDILNNEMSIHNHYIRGLQITQKELQNARPTLANKSYTSYMLAEGFKGSIKEVAAAVLSCGWSYLVIAQNLSQIPNALEHAFYGHWIKGYSSKEFQACVNWNINLLDSLTLTSSKQEIEKLKDIFITTSEYEYLFWDMAYQS 217
               SCOP domains d2rd3d_ D: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rd3 D   0 TMQVSQYLYQNAQSIWGDCISHPFVQGIGRGTLERDKFRFYIIQDYLFLLEYAKVFALGVVKACDEAVMREFSNAIQDILNNEMSIHNHYIRELQITQKELQNACPTLANKSYTSYMLAEGFKGSIKEVAAAVLSCGWSYLVIAQNLSQIPNALEHAFYGHWIKGYSSKEFQACVNWNINLLDSLTLASSKQEIEKLKEIFITTSEYEYLFWDMAYQS 217
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209        


Chain D from PDB  Type:PROTEIN  Length:218
 aligned with TENA_HELPX | A8KRL3 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:218
                             1                                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209        
           TENA_HELPX     - -MQVSQYLYQNAQSIWGDCISHPFVQGIGRGTLERDKFRFYIIQDYLFLLEYAKVFALGVVKACDEAVMREFSNAIQDILNNEMSIHNHYIRELQITQKELQNACPTLANKSYTSYMLAEGFKGSIKEVAAAVLSCGWSYLVIAQNLSQIPNALEHAFYGHWIKGYSSKEFQACVNWNINLLDSLTLASSKQEIEKLKEIFITTSEYEYLFWDMAYQS 217
               SCOP domains d2rd3d_ D: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rd3 D   0 TMQVSQYLYQNAQSIWGDCISHPFVQGIGRGTLERDKFRFYIIQDYLFLLEYAKVFALGVVKACDEAVMREFSNAIQDILNNEMSIHNHYIRELQITQKELQNACPTLANKSYTSYMLAEGFKGSIKEVAAAVLSCGWSYLVIAQNLSQIPNALEHAFYGHWIKGYSSKEFQACVNWNINLLDSLTLASSKQEIEKLKEIFITTSEYEYLFWDMAYQS 217
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2RD3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2RD3)

(-) Gene Ontology  (5, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,D   (O25874_HELPY | O25874)
molecular function
    GO:0050334    thiaminase activity    Catalysis of the reaction: H(2)O + thiamine = 4-amino-5-hydroxymethyl-2-methylpyrimidine + 5-(2-hydroxyethyl)-4-methylthiazole + H(+).
biological process
    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.

Chain A,D   (TENA_HELPX | A8KRL3)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0050334    thiaminase activity    Catalysis of the reaction: H(2)O + thiamine = 4-amino-5-hydroxymethyl-2-methylpyrimidine + 5-(2-hydroxyethyl)-4-methylthiazole + H(+).
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.
    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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TENA_HELPX | A8KRL3: 3ibx

(-) Related Entries Specified in the PDB File

1rtw TENA HOMOLOGUE (PF1337) FROM PYROCOCCUS FURIOSUS
1to9 THI-4 PROTEIN FROM BACILLUS SUBTILIS
1tyh TENA FROM BACILLUS SUBTILIS
1udd TENA HOMOLOGUE FROM P. HORIKOSHII