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(-) Description

Title :  CRYSTAL STRUCTURE OF TT0473, PUTATIVE TRIOSEPHOSPHATE ISOMERASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  H. Yamamoto, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  24 Feb 05  (Deposition) - 15 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Triosephosphate Isomerase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yamamoto, N. Kunishima
Crystal Structure Of Tt0473, Putative Triosephosphate Isomerase From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: PUTATIVE TRIOSEPHOSPHATE ISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
2PO47Ligand/IonPHOSPHATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:222 , MET A:224 , VAL A:227 , HOH A:2075 , HOH A:2137 , HOH A:2170BINDING SITE FOR RESIDUE NA A 1001
2AC2SOFTWARELEU B:222 , MET B:224 , VAL B:227 , HOH B:2132 , HOH B:2133 , HOH B:2234BINDING SITE FOR RESIDUE NA B 1002
3AC3SOFTWARESER A:17 , ARG A:20 , HOH A:2041 , HOH A:2050 , HOH A:2091 , HOH A:2274 , HOH A:2345 , HOH A:2395BINDING SITE FOR RESIDUE PO4 A 2001
4AC4SOFTWAREHOH A:2077 , SER B:17 , ARG B:20 , HOH B:2039 , HOH B:2273 , HOH B:2347 , HOH B:2348BINDING SITE FOR RESIDUE PO4 B 2002
5AC5SOFTWAREGLU A:70 , ARG A:80 , HIS B:13 , LYS B:14 , HOH B:2026 , HOH B:2366BINDING SITE FOR RESIDUE PO4 B 2003
6AC6SOFTWAREALA A:170 , ILE A:171 , GLY A:172 , SER A:212 , GLY A:233 , GLY A:234 , HOH A:2017 , HOH A:2054 , HOH A:2055 , HOH A:2271 , HOH A:2309BINDING SITE FOR RESIDUE PO4 A 2004
7AC7SOFTWAREILE B:171 , GLY B:172 , SER B:212 , GLY B:233 , GLY B:234 , HOH B:2030 , HOH B:2037 , HOH B:2054 , HOH B:2208 , HOH B:2275BINDING SITE FOR RESIDUE PO4 B 2005
8AC8SOFTWAREHIS A:68 , LYS A:69 , GLU A:70 , HOH A:2099 , HOH A:2396BINDING SITE FOR RESIDUE PO4 A 2006
9AC9SOFTWAREHIS A:13 , LYS A:14 , HOH A:2033 , ARG B:80BINDING SITE FOR RESIDUE PO4 A 2007

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TIM_2PS51440 Triosephosphate isomerase (TIM) family profile.TPIS_THET83-248
 		  2A:3-248
B:3-248
2TIM_1PS00171 Triosephosphate isomerase active site.TPIS_THET8164-174
 		  2A:164-174
B:164-174

(-) Exons   (0, 0)

(no "Exon" information available for 1YYA)

(-) 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:250
 aligned with TPIS_THET8 | Q5SJR1 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
           TPIS_THET8     1 MRRVLVAGNWKMHKTPSEARVWFAELKRLLPPLQSEAAVLPAFPILPVAKEVLAETQVGYGAQDVSAHKEGAYTGEVSARMLSDLGCRYAIVGHSERRRYHGETDALVAEKAKRLLEEGITPILCVGEPLEVREKGEAVPYTLRQLRGSLEGVEPPGPEALVIAYEPVWAIGTGKNATPEDAEAMHQAIRKALSERYGEAFASRVRILYGGSVNPKNFADLLSMPNVDGGLVGGASLELESFLALLRIAG 250
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1yyaA00 A:1-250 Aldolase class I                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhh......hhhh.eeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhh.....eeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --TIM_2  PDB: A:3-248 UniProt: 3-248                                                                                                                                                                                                                    -- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      ---------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yya A   1 MRRVLVAGNWKMHKTPSEARVWFAELKRLLPPLQSEAAVLPAFPILPVAKEVLAETQVGYGAQDVSAHKEGAYTGEVSARMLSDLGCRYAIVGHSERRRYHGETDALVAEKAKRLLEEGITPILCVGEPLEVREKGEAVPYTLRQLRGSLEGVEPPGPEALVIAYEPVWAIGTGKNATPEDAEAMHQAIRKALSERYGEAFASRVRILYGGSVNPKNFADLLSMPNVDGGLVGGASLELESFLALLRIAG 250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250


Chain B from PDB  Type:PROTEIN  Length:250
 aligned with TPIS_THET8 | Q5SJR1 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
           TPIS_THET8     1 MRRVLVAGNWKMHKTPSEARVWFAELKRLLPPLQSEAAVLPAFPILPVAKEVLAETQVGYGAQDVSAHKEGAYTGEVSARMLSDLGCRYAIVGHSERRRYHGETDALVAEKAKRLLEEGITPILCVGEPLEVREKGEAVPYTLRQLRGSLEGVEPPGPEALVIAYEPVWAIGTGKNATPEDAEAMHQAIRKALSERYGEAFASRVRILYGGSVNPKNFADLLSMPNVDGGLVGGASLELESFLALLRIAG 250
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1yyaB00 B:1-250 Aldolase class I                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhh...eeeee...............hhhhhhhh...eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhh......hhhh.eeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhh.....eeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --TIM_2  PDB: B:3-248 UniProt: 3-248                                                                                                                                                                                                                    -- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      ---------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yya B   1 MRRVLVAGNWKMHKTPSEARVWFAELKRLLPPLQSEAAVLPAFPILPVAKEVLAETQVGYGAQDVSAHKEGAYTGEVSARMLSDLGCRYAIVGHSERRRYHGETDALVAEKAKRLLEEGITPILCVGEPLEVREKGEAVPYTLRQLRGSLEGVEPPGPEALVIAYEPVWAIGTGKNATPEDAEAMHQAIRKALSERYGEAFASRVRILYGGSVNPKNFADLLSMPNVDGGLVGGASLELESFLALLRIAG 250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   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 1YYA)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YYA)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TPIS_THET8 | Q5SJR1)
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:0004807    triose-phosphate isomerase activity    Catalysis of the reaction: D-glyceraldehyde 3-phosphate = glycerone phosphate.
biological process
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    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.
    GO:0006098    pentose-phosphate shunt    The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.
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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