Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  TRIOSEPHOSPHATE ISOMERASE DRINKS WATER TO KEEP HEALTHY
 
Authors :  Z. Zhang, S. Sugio, E. A. Komives, K. D. Liu, A. M. Stock, N. Narayana, Ng. J. R. Knowles, G. A. Petsko, D. Ringe
Date :  07 Nov 94  (Deposition) - 20 Apr 95  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isomerase(Intramolecular Oxidoreductase) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Zhang, E. A. Komives, S. Sugio, S. C. Blacklow, N. Narayana, N. H. Xuong, A. M. Stock, G. A. Petsko, D. Ringe
The Role Of Water In The Catalytic Efficiency Of Triosephosphate Isomerase.
Biochemistry V. 38 4389 1999
PubMed-ID: 10194358  |  Reference-DOI: 10.1021/BI9826759

(-) Compounds

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
    ChainsA, B
    EC Number5.3.1.1
    EngineeredYES
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PGH2Ligand/IonPHOSPHOGLYCOLOHYDROXAMIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:11 , LYS A:13 , HIS A:95 , GLU A:165 , ALA A:169 , ILE A:170 , GLY A:171 , GLY A:210 , SER A:211 , LEU A:230 , GLY A:232 , GLY A:233 , HOH A:648 , HOH A:673 , HOH A:726 , HOH A:777BINDING SITE FOR RESIDUE PGH A 250
2AC2SOFTWAREASN B:11 , LYS B:13 , HIS B:95 , GLU B:165 , ALA B:169 , ILE B:170 , GLY B:171 , GLY B:210 , SER B:211 , LEU B:230 , GLY B:232 , GLY B:233 , HOH B:692 , HOH B:710 , HOH B:800 , HOH B:856BINDING SITE FOR RESIDUE PGH B 250
3ACAUNKNOWNGLU A:165 , HIS A:95 , PRO A:96 , LYS A:13NULL
4ACBUNKNOWNGLU B:165 , HIS B:95 , PRO B:96 , LYS B:13NULL

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TIM_2PS51440 Triosephosphate isomerase (TIM) family profile.TPIS_CHICK5-246
 
  2A:5-246
B:5-246
2TIM_1PS00171 Triosephosphate isomerase active site.TPIS_CHICK163-173
 
  2A:163-173
B:163-173

(-) Exons   (7, 14)

Asymmetric/Biological Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSGALT000000234421ENSGALE00000242044chr1:80431223-80431451229TPIS_CHICK1-38382A:4-38
B:4-38
35
35
1.2ENSGALT000000234422ENSGALE00000153292chr1:80432287-80432410124TPIS_CHICK38-79422A:38-79
B:38-79
42
42
1.3ENSGALT000000234423ENSGALE00000153290chr1:80432505-8043258985TPIS_CHICK79-107292A:79-107
B:79-107
29
29
1.4ENSGALT000000234424ENSGALE00000153291chr1:80432725-80432857133TPIS_CHICK108-152452A:108-152
B:108-152
45
45
1.5ENSGALT000000234425ENSGALE00000153294chr1:80433088-8043317386TPIS_CHICK152-180292A:152-180
B:152-180
29
29
1.6ENSGALT000000234426ENSGALE00000153293chr1:80433324-8043341188TPIS_CHICK181-210302A:181-210
B:181-210
30
30
1.7ENSGALT000000234427ENSGALE00000153295chr1:80433666-80434223558TPIS_CHICK210-248392A:210-248
B:210-248
39
39

(-) 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:245
 aligned with TPIS_CHICK | P00940 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:245
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243     
           TPIS_CHICK     4 RKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFARQKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGESDELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRIIYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH 248
               SCOP domains d1tpwa_ A: Triosephosphate isomerase                                                                                                                                                                                                                  SCOP domains
               CATH domains 1tpwA00 A:4-248 Aldolase class I                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhh......eeeeeee....hhhhhhh.....eeee................hhhhhhh...eeee..hhhhh.....hhhhhhhhhhhhh...eeeeee...hhhhh...hhhhhhhhhhhhh........eeeee..........hhhhhhhhhhhhhhhhhh.....hhhhhh..eee........hhhhh......eeee........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -TIM_2  PDB: A:5-246 UniProt: 5-246                                                                                                                                                                                                                -- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:4-38 UniProt: 1-38----------------------------------------Exon 1.3  PDB: A:79-107      Exon 1.4  PDB: A:108-152 UniProt: 108-152    ----------------------------Exon 1.6  PDB: A:181-210      -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.2  PDB: A:38-79 UniProt: 38-79     ------------------------------------------------------------------------Exon 1.5  PDB: A:152-180     -----------------------------Exon 1.7  PDB: A:210-248                Transcript 1 (2)
                 1tpw A   4 RKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFARQKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHPERRHVFGESDELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKTHVSDAVAQSTRIIYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH 248
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243     

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with TPIS_CHICK | P00940 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:245
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243     
           TPIS_CHICK     4 RKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFARQKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGESDELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRIIYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH 248
               SCOP domains d1tpwb_ B: Triosephosphate isomerase                                                                                                                                                                                                                  SCOP domains
               CATH domains 1tpwB00 B:4-248 Aldolase class I                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) --TIM-1tpwB01 B:6-244                                                                                                                                                                                                                            ---- Pfam domains (1)
           Pfam domains (2) --TIM-1tpwB02 B:6-244                                                                                                                                                                                                                            ---- Pfam domains (2)
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhh......eeeeeee....hhhhhhh.....eeee................hhhhhhh...eeee..hhhhh.....hhhhhhhhhhhhh...eeeeee...hhhhh...hhhhhhhhhhhhh........eeeee..........hhhhhhhhhhhhhhhhhh.....hhhhhh..eeee.......hhhhh......eeee........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -TIM_2  PDB: B:5-246 UniProt: 5-246                                                                                                                                                                                                                -- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: B:4-38 UniProt: 1-38----------------------------------------Exon 1.3  PDB: B:79-107      Exon 1.4  PDB: B:108-152 UniProt: 108-152    ----------------------------Exon 1.6  PDB: B:181-210      -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.2  PDB: B:38-79 UniProt: 38-79     ------------------------------------------------------------------------Exon 1.5  PDB: B:152-180     -----------------------------Exon 1.7  PDB: B:210-248                Transcript 1 (2)
                 1tpw B   4 RKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFARQKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHPERRHVFGESDELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKTHVSDAVAQSTRIIYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH 248
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243     

   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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TPIS_CHICK | P00940)
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.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    GO:0046166    glyceraldehyde-3-phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of glyceraldehyde-3-phosphate, an important intermediate in glycolysis.
    GO:0019682    glyceraldehyde-3-phosphate metabolic process    The chemical reactions and pathways involving glyceraldehyde-3-phosphate, an important intermediate in glycolysis.
    GO:0019563    glycerol catabolic process    The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
    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:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    PGH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    ACA  [ RasMol ]  +environment [ RasMol ]
    ACB  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1tpw)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1tpw
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TPIS_CHICK | P00940
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  5.3.1.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  TPIS_CHICK | P00940
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TPIS_CHICK | P009401spq 1sq7 1ssd 1ssg 1su5 1sw0 1sw3 1sw7 1tim 1tpb 1tpc 1tph 1tpu 1tpv 4p61 8tim

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1TPW)