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(-) Description

Title :  TENA HOMOLOG/THI-4 THIAMINASE COMPLEXED WITH PRODUCT 4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE
 
Authors :  M. R. Sawaya, S. Chan, G. W. Han, L. J. Perry, I. Pashkov
Date :  06 Apr 06  (Deposition) - 18 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Thiaminase, Transcription, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Sawaya, S. Chan, G. W. Han, I. Pashkov, L. J. Perry, T. O. Yeates
Crystal Structure Of A Tena Homolog/Thi-4 Thiaminase From Pyrobaculum Aerophilum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TENA HOMOLOG/THI-4 THIAMINASE
    Chains: A, B, C, D
    EC Number: 2.5.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCHIS-2-TOPO
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TENA/THI4 (PAG5_170)
    Organism Scientific: PYROBACULUM AEROPHILUM
    Organism Taxid: 178306
    Strain: STR. IM2

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2HMH4Ligand/Ion4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:43 , TYR A:46 , LEU A:47 , GLU A:81 , TYR A:85 , CYS A:134 , TYR A:138 , TYR A:169 , GLU A:201 , PHE A:204BINDING SITE FOR RESIDUE HMH A 301
2AC2SOFTWAREASP B:43 , TYR B:46 , LEU B:47 , GLU B:81 , CYS B:134 , TYR B:138 , TYR B:169 , GLU B:201 , PHE B:204BINDING SITE FOR RESIDUE HMH B 302
3AC3SOFTWAREASP C:43 , TYR C:46 , LEU C:47 , GLU C:81 , CYS C:134 , TYR C:138 , TYR C:169 , GLU C:201BINDING SITE FOR RESIDUE HMH C 303
4AC4SOFTWAREASP D:43 , TYR D:46 , LEU D:47 , GLU D:81 , CYS D:134 , TYR D:138 , TYR D:169 , GLU D:201 , HOH D:314BINDING SITE FOR RESIDUE HMH D 304
5AC5SOFTWARESER A:110 , GLU A:203 , SER C:110 , GLU C:203BINDING SITE FOR RESIDUE EDO A 305
6AC6SOFTWARETYR B:200 , GLU B:203 , SER D:110 , GLU D:203BINDING SITE FOR RESIDUE EDO D 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GM8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GM8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GM8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GM8)

(-) Exons   (0, 0)

(no "Exon" information available for 2GM8)

(-) 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:217
 aligned with Q8ZZM9_PYRAE | Q8ZZM9 from UniProtKB/TrEMBL  Length:212

    Alignment length:217
                                 1                                                                                                                                                                                                                   
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       
         Q8ZZM9_PYRAE     - -----MVTGELRRRADGIWQRILAHPFVAELYAGTLPMEKFKYYLLQDYNYLVNFAKALSLAASRAPSVDLMKTALELAYGTVTGEMANYEALLKEVGLSLRDAAEAEPNRVNVSYMAYLKSTCALEGFYQCMAALLPCFWSYAEIAERHGGKLRENPVHVYKKWASVYLSPEYRGLVERLRAVLDSSGLSAEELWPYFKEASLYELEFWQAAYEGH 212
               SCOP domains d2gm8a_ A: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains 2gm8A00 A:-4-212 Heme Oxygenase; Chain A                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gm8 A  -4 HHHHHGVTGELRRRADGIWQRILAHPFVAELYAGTLPMEKFKYYLLQDYNYLVNFAKALSLAASRAPSVDLMKTALELAYGTVTGEMANYEALLKEVGLSLRDAAEAEPNRVNVSYMAYLKSTCALEGFYQCMAALLPCFWSYAEIAERHGGKLRENPVHVYKKWASVYLSPEYRGLVERLRAVLDSSGLSAEELWPYFKEASLYELEFWQAAYEGH 212
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with Q8ZZM9_PYRAE | Q8ZZM9 from UniProtKB/TrEMBL  Length:212

    Alignment length:213
                             1                                                                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209   
         Q8ZZM9_PYRAE     - -MVTGELRRRADGIWQRILAHPFVAELYAGTLPMEKFKYYLLQDYNYLVNFAKALSLAASRAPSVDLMKTALELAYGTVTGEMANYEALLKEVGLSLRDAAEAEPNRVNVSYMAYLKSTCALEGFYQCMAALLPCFWSYAEIAERHGGKLRENPVHVYKKWASVYLSPEYRGLVERLRAVLDSSGLSAEELWPYFKEASLYELEFWQAAYEGH 212
               SCOP domains d2gm8b_ B: automated matches                                                                                                                                                                                          SCOP domains
               CATH domains 2gm8B00 B:0-212 Heme Oxygenase; Chain A                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gm8 B   0 HGVTGELRRRADGIWQRILAHPFVAELYAGTLPMEKFKYYLLQDYNYLVNFAKALSLAASRAPSVDLMKTALELAYGTVTGEMANYEALLKEVGLSLRDAAEAEPNRVNVSYMAYLKSTCALEGFYQCMAALLPCFWSYAEIAERHGGKLRENPVHVYKKWASVYLSPEYRGLVERLRAVLDSSGLSAEELWPYFKEASLYELEFWQAAYEGH 212
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209   


Chain C from PDB  Type:PROTEIN  Length:215
 aligned with Q8ZZM9_PYRAE | Q8ZZM9 from UniProtKB/TrEMBL  Length:212

    Alignment length:215
                               1                                                                                                                                                                                                                   
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207     
         Q8ZZM9_PYRAE     - ---MVTGELRRRADGIWQRILAHPFVAELYAGTLPMEKFKYYLLQDYNYLVNFAKALSLAASRAPSVDLMKTALELAYGTVTGEMANYEALLKEVGLSLRDAAEAEPNRVNVSYMAYLKSTCALEGFYQCMAALLPCFWSYAEIAERHGGKLRENPVHVYKKWASVYLSPEYRGLVERLRAVLDSSGLSAEELWPYFKEASLYELEFWQAAYEGH 212
               SCOP domains d2gm8c_ C: automated matches                                                                                                                                                                                            SCOP domains
               CATH domains 2gm8C00 C:-2-212 Heme Oxygenase; Chain A                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gm8 C  -2 HHHGVTGELRRRADGIWQRILAHPFVAELYAGTLPMEKFKYYLLQDYNYLVNFAKALSLAASRAPSVDLMKTALELAYGTVTGEMANYEALLKEVGLSLRDAAEAEPNRVNVSYMAYLKSTCALEGFYQCMAALLPCFWSYAEIAERHGGKLRENPVHVYKKWASVYLSPEYRGLVERLRAVLDSSGLSAEELWPYFKEASLYELEFWQAAYEGH 212
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207     


Chain D from PDB  Type:PROTEIN  Length:217
 aligned with Q8ZZM9_PYRAE | Q8ZZM9 from UniProtKB/TrEMBL  Length:212

    Alignment length:217
                                 1                                                                                                                                                                                                                   
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       
         Q8ZZM9_PYRAE     - -----MVTGELRRRADGIWQRILAHPFVAELYAGTLPMEKFKYYLLQDYNYLVNFAKALSLAASRAPSVDLMKTALELAYGTVTGEMANYEALLKEVGLSLRDAAEAEPNRVNVSYMAYLKSTCALEGFYQCMAALLPCFWSYAEIAERHGGKLRENPVHVYKKWASVYLSPEYRGLVERLRAVLDSSGLSAEELWPYFKEASLYELEFWQAAYEGH 212
               SCOP domains d2gm8d_ D: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains 2gm8D00 D:-4-212 Heme Oxygenase; Chain A                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gm8 D  -4 HHHHHGVTGELRRRADGIWQRILAHPFVAELYAGTLPMEKFKYYLLQDYNYLVNFAKALSLAASRAPSVDLMKTALELAYGTVTGEMANYEALLKEVGLSLRDAAEAEPNRVNVSYMAYLKSTCALEGFYQCMAALLPCFWSYAEIAERHGGKLRENPVHVYKKWASVYLSPEYRGLVERLRAVLDSSGLSAEELWPYFKEASLYELEFWQAAYEGH 212
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205
   Legend:   → Mismatch (orange background)
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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, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GM8)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q8ZZM9_PYRAE | Q8ZZM9)
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.

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  2.5.1.2
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 Related Entries

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

UniProtKB/TrEMBL
        Q8ZZM9_PYRAE | Q8ZZM9: 2gm7

(-) Related Entries Specified in the PDB File

2gm7 TENA HOMOLOG/THI-4 THIAMINASE FROM PYROBACULUM AEROPHILUM