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(-) Description

Title :  STRUCTURE OF E97D MUTANT OF TIM FROM PLASMODIUM FALCIPARUM
 
Authors :  M. Samanta, M. R. N. Murthy, H. Balaram, P. Balaram
Date :  02 Dec 10  (Deposition) - 19 Oct 11  (Release) - 19 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrel, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Samanta, M. R. N. Murthy, H. Balaram, P. Balaram
Revisiting The Mechanism Of The Triosephosphate Isomerase Reaction: The Role Of The Fully Conserved Glutamic Acid 97 Residue
Chembiochem V. 12 1886 2011
PubMed-ID: 21671330  |  Reference-DOI: 10.1002/CBIC.201100116

(-) Compounds

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
    ChainsA, B
    EC Number5.3.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTRC99A
    Expression System StrainAA200
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneTPI
    MutationYES
    Organism ScientificPLASMODIUM FALCIPARUM
    Organism Taxid5833
    SynonymTIM, TRIOSE-PHOSPHATE ISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2SO43Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:211 , GLY A:232 , ASN A:233 , EDO A:250 , HOH A:306 , HOH A:428 , HOH A:431BINDING SITE FOR RESIDUE SO4 A 249
2AC2SOFTWAREASN A:10 , LYS A:12 , HIS A:95 , LEU A:230 , GLY A:232 , SO4 A:249 , HOH A:284 , HOH A:287BINDING SITE FOR RESIDUE EDO A 250
3AC3SOFTWARELYS B:12 , GLY B:232 , ASN B:233 , EDO B:250 , HOH B:340 , HOH B:458BINDING SITE FOR RESIDUE SO4 B 249
4AC4SOFTWAREASN B:10 , LYS B:12 , HIS B:95 , GLY B:209 , LEU B:230 , VAL B:231 , GLY B:232 , SO4 B:249 , HOH B:261 , HOH B:275BINDING SITE FOR RESIDUE EDO B 250
5AC5SOFTWARECYS A:196 , ARG B:52 , LYS B:53 , LEU B:55BINDING SITE FOR RESIDUE SO4 B 251

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PSV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PSV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PSV)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TIM_2PS51440 Triosephosphate isomerase (TIM) family profile.TPIS_PLAFA4-246
 
  2A:4-246
B:4-246
2TIM_1PS00171 Triosephosphate isomerase active site.TPIS_PLAFA163-173
 
  2A:164-171
B:164-173

(-) Exons   (0, 0)

(no "Exon" information available for 3PSV)

(-) 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_PLAFA | Q07412 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:246
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
           TPIS_PLAFA     3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILAYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
               SCOP domains d3psva_ A: Triosephosphate isomerase                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhh.....eeeee.hhhhh.---..hhhhhhhhhhhhhhhhhhhhhhhhhhhheeee.......hhhhhhh.....eeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -TIM_2  PDB: A:4-246 UniProt: 4-246                                                                                                                                                                                                                 -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3psv A   3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFDRRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLWAIG---TATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        |-  |    182       192       202       212       222       232       242      
                                                                                                                                                                                                  171 175                                                                         

Chain B from PDB  Type:PROTEIN  Length:244
 aligned with TPIS_PLAFA | Q07412 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:246
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      
           TPIS_PLAFA     3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILAYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
               SCOP domains d3psvb_ B: Triosephosphate isomerase                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhh....eeee...............hhhhhhhh...eeee.hhhhhhhh..hhhhhhhhhhhhhhh..eeeeee..hhhhhhh.hhhhhhhhhhhhhhhhh.....eeeee.....--.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhh.....eeeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -TIM_2  PDB: B:4-246 UniProt: 4-246                                                                                                                                                                                                                 -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3psv B   3 RKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFDRRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLWA--TGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162      |172       182       192       202       212       222       232       242      
                                                                                                                                                                                                169  |                                                                            
                                                                                                                                                                                                   172                                                                            

   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  (0, 0)

(no "CATH Domain" information available for 3PSV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PSV)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TPIS_PLAFA | Q07412)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TPIS_PLAFA | Q074121lyx 1lzo 1m7o 1m7p 1o5x 1vga 1woa 1wob 1ydv 2fi6 2vfd 2vfe 2vff 2vfg 2vfh 2vfi 3psw 3pvf 3pwa 3py2 4ywi 4yxg 4z0j 4z0s 4zz9 5bmw 5bmx 5bnk 5brb

(-) Related Entries Specified in the PDB File

3psw E97Q MUTANT