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(-) Description

Title :  CRYSTAL STRUCTURE OF TTHB049 FROM THERMUS THERMOPHILUS HB8
 
Authors :  M. Sugahara, Y. Matsuura, Y. Morikawa, H. Shimada, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  19 Mar 07  (Deposition) - 25 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Thermus Thermophilus Hb8, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sugahara, Y. Matsuura, Y. Morikawa, H. Shimada, N. Kunishima
Crystal Structure Of Tthb049 From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALPHA-RIBAZOLE-5'-PHOSPHATE PHOSPHATASE
    Chains: A, B
    EC Number: 3.1.3.73
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Synonym: TTHB049 PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:79 , GLU A:81 , ALA B:79 , GLU B:81BINDING SITE FOR RESIDUE NA B 2001
2AC2SOFTWAREPHE A:120 , GLY A:123 , LEU A:124BINDING SITE FOR RESIDUE GOL A 1001
3AC3SOFTWAREPHE B:48 , PHE B:120 , GLY B:123 , LEU B:124 , HOH B:2015BINDING SITE FOR RESIDUE GOL B 1002
4AC4SOFTWAREGLU A:74 , ILE A:75 , PHE A:77 , PHE A:99 , GLY A:135 , ARG A:138BINDING SITE FOR RESIDUE GOL A 1003
5AC5SOFTWAREGLU B:74 , ILE B:75 , LEU B:96 , GLY B:135 , ARG B:138BINDING SITE FOR RESIDUE GOL B 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P6M)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Trp A:160 -Pro A:161
2Trp B:160 -Pro B:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P6M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P6M)

(-) Exons   (0, 0)

(no "Exon" information available for 2P6M)

(-) 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:171
 aligned with Q53WB3_THET8 | Q53WB3 from UniProtKB/TrEMBL  Length:177

    Alignment length:171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 
         Q53WB3_THET8     1 MELWLVRHGETLWNREGRLLGWTDLPLTAEGEAQARRLKGALPSLPAFSSDLLRARRTAELAGFSPRLYPELREIHFGALEGALWETLDPRYKEALLRFQGFHPPGGESLSAFQERVFRFLEGLKAPAVLFTHGGVVRAVLRALGEDGLVPPGSAVAVDWPRRVLVRLALD 171
               SCOP domains d2p6ma_ A: automated matches                                                                                                                                                SCOP domains
               CATH domains 2p6mA00 A:1-171 Phosphoglycerate mutase-like                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhh..........hhhhhhhhhhhh.......eee..hhhhhhhhhhh....ee.hhhh...hhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhh..........eeeee...eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p6m A   1 MELWLVRHGETLWNREGRLLGWTDMPLTAEGEAQARRLKGALPSLPAFSSDLLRARRTAELAGFSPRLYPELREIHFGALEGALWETLDPRYKEALLRFQGFHPPGGESLSAFQERVFRFLEGLKAPAVLFTHGGVVRAVLRALGEDGLVPPGSAVAVDWPRRVLVRLALD 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 


Chain B from PDB  Type:PROTEIN  Length:170
 aligned with Q53WB3_THET8 | Q53WB3 from UniProtKB/TrEMBL  Length:177

    Alignment length:170
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
         Q53WB3_THET8     1 MELWLVRHGETLWNREGRLLGWTDLPLTAEGEAQARRLKGALPSLPAFSSDLLRARRTAELAGFSPRLYPELREIHFGALEGALWETLDPRYKEALLRFQGFHPPGGESLSAFQERVFRFLEGLKAPAVLFTHGGVVRAVLRALGEDGLVPPGSAVAVDWPRRVLVRLAL 170
               SCOP domains d2p6mb_ B: automated matches                                                                                                                                               SCOP domains
               CATH domains 2p6mB00 B:1-170 Phosphoglycerate mutase-like                                                                                                                               CATH domains
           Pfam domains (1) -His_Phos_1-2p6mB01 B:2-140                                                                                                                 ------------------------------ Pfam domains (1)
           Pfam domains (2) -His_Phos_1-2p6mB02 B:2-140                                                                                                                 ------------------------------ Pfam domains (2)
         Sec.struct. author .eeeeee...hhhhhhh..........hhhhhhhhhhhh.......eee..hhhhhhhhhhh....ee.hhhh...hhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh..........eeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p6m B   1 MELWLVRHGETLWNREGRLLGWTDMPLTAEGEAQARRLKGALPSLPAFSSDLLRARRTAELAGFSPRLYPELREIHFGALEGALWETLDPRYKEALLRFQGFHPPGGESLSAFQERVFRFLEGLKAPAVLFTHGGVVRAVLRALGEDGLVPPGSAVAVDWPRRVLVRLAL 170
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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, 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: PGM (50)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q53WB3_THET8 | Q53WB3)
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.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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 Related Entries

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

UniProtKB/TrEMBL
        Q53WB3_THET8 | Q53WB3: 1v37 1v7q 2ekb 2ekz 2enu 2enw 2eoa 2hia 2owd 2owe 2p2y 2p2z 2p30 2p6o 2p75 2p77 2p78 2p79 2p9f 2p9y 2p9z 2pa0

(-) Related Entries Specified in the PDB File

2p6o
2p75
2p77
2p78
2p79 RELATED ID: TTK003000215.15 RELATED DB: TARGETDB