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(-) Description

Title :  STRUCTURE OF TENI FROM BACILLUS SUBTILIS
 
Authors :  A. V. Toms, A. L. Haas, J. -H. Park, T. P. Begley, S. E. Ealick
Date :  17 Dec 04  (Deposition) - 22 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Tim Barrel, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. V. Toms, A. L. Haas, J. H. Park, T. P. Begley, S. E. Ealick
Structural Characterization Of The Regulatory Proteins Tena And Teni From Bacillus Subtilis And Identification Of Tena As A Thiaminase Ii.
Biochemistry V. 44 2319 2005
PubMed-ID: 15709744  |  Reference-DOI: 10.1021/BI0478648
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATORY PROTEIN TENI
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TENI
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
11443Ligand/IonTRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2SO48Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
11442Ligand/IonTRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
11441Ligand/IonTRIS-HYDROXYMETHYL-METHYL-AMMONIUM
2SO44Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:156 , MET A:176 , SER A:177 , GLY A:178 , HOH A:2025 , HOH A:2184 , HOH A:2287 , HOH A:2567BINDING SITE FOR RESIDUE SO4 A 291
02AC2SOFTWAREGLY B:156 , MET B:176 , SER B:177 , GLY B:178 , HOH B:2009 , HOH B:2187 , HOH B:2279 , HOH B:2385 , HOH B:2444BINDING SITE FOR RESIDUE SO4 B 292
03AC3SOFTWAREGLY C:156 , MET C:176 , SER C:177 , GLY C:178 , HOH C:2042 , HOH C:2528 , HOH C:2563BINDING SITE FOR RESIDUE SO4 C 293
04AC4SOFTWAREGLY D:155 , GLY D:156 , VAL D:175 , MET D:176 , SER D:177 , HOH D:2020 , HOH D:2090 , HOH D:2307 , HOH D:2461BINDING SITE FOR RESIDUE SO4 D 294
05AC5SOFTWAREGLY A:63 , PRO A:79 , HOH A:2000 , SER B:38 , ALA B:39 , ARG B:64 , HOH B:2003 , HOH B:2135 , HOH B:2290 , HOH B:2526BINDING SITE FOR RESIDUE SO4 B 295
06AC6SOFTWARESER A:38 , ALA A:39 , ARG A:64 , HOH A:2070 , HOH A:2221 , HOH A:2414 , HOH A:2417 , GLY B:63 , PRO B:79 , HOH B:2005BINDING SITE FOR RESIDUE SO4 A 296
07AC7SOFTWARESER C:38 , ALA C:39 , ARG C:64 , HOH C:2072 , HOH C:2303 , HOH C:2333 , GLY D:63 , PRO D:79 , HOH D:2026 , HOH D:2202BINDING SITE FOR RESIDUE SO4 C 297
08AC8SOFTWAREGLY C:63 , ARG C:64 , PRO C:79 , HOH C:2014 , HOH C:2555 , SER D:38 , ALA D:39 , ARG D:64 , HOH D:2027 , HOH D:2387BINDING SITE FOR RESIDUE SO4 D 298
09AC9SOFTWAREARG A:33 , ARG A:35 , ASN A:62 , PRO A:79 , SER A:80 , SER A:100 , HIS A:102BINDING SITE FOR RESIDUE 144 A 300
10BC1SOFTWAREARG B:33 , ARG B:35 , ASN B:62 , PRO B:79 , SER B:80 , SER B:100 , HIS B:102BINDING SITE FOR RESIDUE 144 B 301
11BC2SOFTWAREARG D:33 , ASN D:62 , PRO D:79 , SER D:80 , SER D:100 , HIS D:102 , HOH D:2235 , HOH D:2259BINDING SITE FOR RESIDUE 144 D 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YAD)

(-) 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:190
 aligned with TENI_BACSU | P25053 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
           TENI_BACSU     1 MELHAITDDSKPVEELARIIITIQNEVDFIHIRERSKSAADILKLLDLIFEGGIDKRKLVMNGRVDIALFSTIHRVQLPSGSFSPKQIRARFPHLHIGRSVHSLEEAVQAEKEDADYVLFGHVFETDCKKGLEGRGVSLLSDIKQRISIPVIAIGGMTPDRLRDVKQAGADGIAVMSGIFSSAEPLEAARRYSRKLKEMR 200
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhh..hhh.eeee.hhhhhhh....eeee.....hhhhhhhhh...eeeeee.hhhhhhhhhhh...eeeee...----------hhhhhhhhhhhhh...eeee...hhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yad A   1 MELHAITDDSKPVEELARIIITIQNEVDFIHIRERSKSAADILKLLDLIFEGGIDKRKLVMNGRVDIALFSTIHRVQLPSGSFSPKQIRARFPHLHIGRSVHSLEEAVQAEKEDADYVLFGHVF----------RGVSLLSDIKQRISIPVIAIGGMTPDRLRDVKQAGADGIAVMSGIFSSAEPLEAARRYSRKLKEMR 200
                                    10        20        30        40        50        60        70        80        90       100       110       120   |     -    |  140       150       160       170       180       190       200
                                                                                                                                                     124        135                                                                 


Chain B from PDB  Type:PROTEIN  Length:193
 aligned with TENI_BACSU | P25053 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
           TENI_BACSU     1 MELHAITDDSKPVEELARIIITIQNEVDFIHIRERSKSAADILKLLDLIFEGGIDKRKLVMNGRVDIALFSTIHRVQLPSGSFSPKQIRARFPHLHIGRSVHSLEEAVQAEKEDADYVLFGHVFETDCKKGLEGRGVSLLSDIKQRISIPVIAIGGMTPDRLRDVKQAGADGIAVMSGIFSSAEPLEAARRYSRKLKEMR 200
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh..hhh.eeee.hhhhhhhh...eeee.....hhhhhhhhh...eeeeee.hhhhhhhhhhh...eeeee...-------...hhhhhhhhhhhhh...eeee...hhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yad B   1 MELHAITDDSKPVEELARIIITIQNEVDFIHIRERSKSAADILKLLDLIFEGGIDKRKLVMNGRVDIALFSTIHRVQLPSGSFSPKQIRARFPHLHIGRSVHSLEEAVQAEKEDADYVLFGHVF-------LEGRGVSLLSDIKQRISIPVIAIGGMTPDRLRDVKQAGADGIAVMSGIFSSAEPLEAARRYSRKLKEMR 200
                                    10        20        30        40        50        60        70        80        90       100       110       120   |     - |     140       150       160       170       180       190       200
                                                                                                                                                     124     132                                                                    


Chain C from PDB  Type:PROTEIN  Length:190
 aligned with TENI_BACSU | P25053 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
           TENI_BACSU     1 MELHAITDDSKPVEELARIIITIQNEVDFIHIRERSKSAADILKLLDLIFEGGIDKRKLVMNGRVDIALFSTIHRVQLPSGSFSPKQIRARFPHLHIGRSVHSLEEAVQAEKEDADYVLFGHVFETDCKKGLEGRGVSLLSDIKQRISIPVIAIGGMTPDRLRDVKQAGADGIAVMSGIFSSAEPLEAARRYSRKLKEMR 200
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhh..hhh.eeee.hhhhhhhh...eeee.....hhhhhhhhh...eeeeee.hhhhhhhhhhh...eeeee...----------hhhhhhhhhhhhh...eeee...hhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yad C   1 MELHAITDDSKPVEELARIIITIQNEVDFIHIRERSKSAADILKLLDLIFEGGIDKRKLVMNGRVDIALFSTIHRVQLPSGSFSPKQIRARFPHLHIGRSVHSLEEAVQAEKEDADYVLFGHVF----------RGVSLLSDIKQRISIPVIAIGGMTPDRLRDVKQAGADGIAVMSGIFSSAEPLEAARRYSRKLKEMR 200
                                    10        20        30        40        50        60        70        80        90       100       110       120   |     -    |  140       150       160       170       180       190       200
                                                                                                                                                     124        135                                                                 


Chain D from PDB  Type:PROTEIN  Length:190
 aligned with TENI_BACSU | P25053 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
           TENI_BACSU     1 MELHAITDDSKPVEELARIIITIQNEVDFIHIRERSKSAADILKLLDLIFEGGIDKRKLVMNGRVDIALFSTIHRVQLPSGSFSPKQIRARFPHLHIGRSVHSLEEAVQAEKEDADYVLFGHVFETDCKKGLEGRGVSLLSDIKQRISIPVIAIGGMTPDRLRDVKQAGADGIAVMSGIFSSAEPLEAARRYSRKLKEMR 200
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --TMP-TENI-1yadD01 D:3-179                                                                                                                                                         --------------------- Pfam domains (1)
           Pfam domains (2) --TMP-TENI-1yadD02 D:3-179                                                                                                                                                         --------------------- Pfam domains (2)
           Pfam domains (3) --TMP-TENI-1yadD03 D:3-179                                                                                                                                                         --------------------- Pfam domains (3)
           Pfam domains (4) --TMP-TENI-1yadD04 D:3-179                                                                                                                                                         --------------------- Pfam domains (4)
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhh..hhh.eeee.hhhhhhh....eeee.....hhhhhhhhh...eeeeee.hhhhhhhhhhh...eeeee...----------hhhhhhhhhhhhh...eeee...hhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yad D   1 MELHAITDDSKPVEELARIIITIQNEVDFIHIRERSKSAADILKLLDLIFEGGIDKRKLVMNGRVDIALFSTIHRVQLPSGSFSPKQIRARFPHLHIGRSVHSLEEAVQAEKEDADYVLFGHVF----------RGVSLLSDIKQRISIPVIAIGGMTPDRLRDVKQAGADGIAVMSGIFSSAEPLEAARRYSRKLKEMR 200
                                    10        20        30        40        50        60        70        80        90       100       110       120   |     -    |  140       150       160       170       180       190       200
                                                                                                                                                     124        135
   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  (0, 0)

(no "SCOP Domain" information available for 1YAD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YAD)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (TENI_BACSU | P25053)
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:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    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: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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

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        TENI_BACSU | P25053: 3qh2

(-) Related Entries Specified in the PDB File

1yaf TRANSCRIPTIONAL ACTIVATOR TENA
1yak