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(-) Description

Title :  UNDERSTANDING PROTEIN LIDS: STRUCTURAL ANALYSIS OF ACTIVE HINGE MUTANTS IN TRIOSEPHOSPHATE ISOMERASE
 
Authors :  I. Kursula, M. Salin, J. Sun, B. V. Norledge, A. M. Haapalainen, N. S. Sam R. K. Wierenga
Date :  17 Mar 04  (Deposition) - 24 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Archae, Evolution, Flexible Loop-6, Tim, N-Hinge, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Kursula, M. Salin, J. Sun, B. V. Norledge, A. M. Haapalainen, N. S. Sampson, R. K. Wierenga
Understanding Protein Lids: Structural Analysis Of Active Hinge Mutants In Triosephosphate Isomerase
Protein Eng. Des. Sel. V. 17 375 2004
PubMed-ID: 15166315  |  Reference-DOI: 10.1093/PROTEIN/GZH048

(-) Compounds

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
    ChainsA, B
    EC Number5.3.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPBSX1C
    Expression System StrainDF502
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneTPI1
    MutationYES
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031
    SynonymTIM

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1PEG3Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:15 , SER A:222 , LYS B:71 , HOH B:1159 , HOH B:1162BINDING SITE FOR RESIDUE PEG B 1001
2AC2SOFTWAREASP A:49 , GLN A:53 , LYS B:18 , ASP B:49 , GLN B:53 , HOH B:1146 , HOH B:1156BINDING SITE FOR RESIDUE PEG B 1002
3AC3SOFTWAREPHE A:102 , VAL B:101 , PHE B:102BINDING SITE FOR RESIDUE PEG A 1003

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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:163-168

(-) Exons   (7, 14)

Asymmetric/Biological Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSGALT000000234421ENSGALE00000242044chr1:80431223-80431451229TPIS_CHICK1-38382A:4-38
B:2-38
35
37
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 (gaps)
B:152-180 (gaps)
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:243
 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 d1spqa_ A: Triosephosphate isomerase                                                                                                                                                                                                                  SCOP domains
               CATH domains 1spqA00 A:4-248 Aldolase class I                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhh...hhh.eeeee......--....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhh.....eeeehhhhhhhhhhhhhh... 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 UniProt: 152-180    -----------------------------Exon 1.7  PDB: A:210-248                Transcript 1 (2)
                 1spq A   4 RKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFARQKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGESDELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDWSKVVLAYEPVWAI--GKTKTPQQAQEVHEKLRGWLKSHVSDAVAQSTRIIYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH 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     
                                                                                                                                                                                                170  |                                                                           
                                                                                                                                                                                                   173                                                                           

Chain B from PDB  Type:PROTEIN  Length:239
 aligned with TPIS_CHICK | P00940 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
           TPIS_CHICK     2 APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFARQKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGESDELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSHVSDAVAQSTRIIYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH 248
               SCOP domains d1spqb_ B: Triosephosphate isomerase                                                                                                                                                                                                                    SCOP domains
               CATH domains 1spqB00 B:2-248 Aldolase class I                                                                                                                                                                                                                        CATH domains
           Pfam domains (1) ----TIM-1spqB01 B:6-244                                                                                                                                                                                                                            ---- Pfam domains (1)
           Pfam domains (2) ----TIM-1spqB02 B:6-244                                                                                                                                                                                                                            ---- Pfam domains (2)
         Sec.struct. author ....eeeeee.....hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhh...hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhh...hhh.eeeee....--------hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhh.....eeeehhhhhhhhhhhhhh... 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:2-38 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 UniProt: 152-180    -----------------------------Exon 1.7  PDB: B:210-248                Transcript 1 (2)
                 1spq B   2 APRKFFVGGNWKMNGDKKSLGELIHTLNGAKLSADTEVVCGAPSIYLDFARQKLDAKIGVAAQNCYKVPKGAFTGEISPAMIKDIGAAWVILGHSERRHVFGESDELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTKAIADNVKDWSKVVLAYEPVW--------TPQQAQEVHEKLRGWLKSHVSDAVAQSTRIIYGGSVTGGNCKELASQHDVDGFLVGGASLKPEFVDIINAKH 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161      |  -     | 181       191       201       211       221       231       241       
                                                                                                                                                                                                168      177                                                                       

   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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TPIS_CHICK | P009401sq7 1ssd 1ssg 1su5 1sw0 1sw3 1sw7 1tim 1tpb 1tpc 1tph 1tpu 1tpv 1tpw 4p61 8tim

(-) Related Entries Specified in the PDB File

1sq7 K174L, T175W MUTANTS
1ssd K174Y, T175S, A176L MUTANTS
1ssg K174Y, T175S, A176L MUTANTS WITH PGA
1su5 K174N, T175P, A176N MUTANTS
1sw0 K174L, T175W MUTANTS WITH PGA
1sw3 T175V MUTANT
1sw7 K174N, T175S, A176S MUTANTS