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(-) Description

Title :  CRYSTAL STRUCTURE OF THE F96S MUTANT OF PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE
 
Authors :  P. Gayathri, M. Banerjee, A. Vijayalakshmi, H. Balaram, P. Balaram, M. R. N. Murthy
Date :  03 Nov 07  (Deposition) - 09 Dec 08  (Release) - 04 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Plasmodium Falciparum, Fatty Acid Biosynthesis, Triosephosphate Isomerase, Pentose Shunt, Gluconeogenesis, Lipid Synthesis, Tim, Mutant, Loop Open, Isomerase, Glycolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Gayathri, M. Banerjee, A. Vijayalakshmi, H. Balaram, P. Balaram, M. R. N. Murthy
Biochemical And Structural Characterization Of Residue 96 Mutants Of Plasmodium Falciparum Triosephosphate Isomerase: Active-Site Loop Conformation, Hydration And Identification Of A Dimer-Interface Ligand-Binding Site.
Acta Crystallogr. , Sect. D V. 65 847 2009
PubMed-ID: 19622869  |  Reference-DOI: 10.1107/S0907444909018666

(-) Compounds

Molecule 1 - TRIOSEPHOSPHATE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PARC1008
    Expression System Strain: AA200
    Expression System Taxid: 562
    Expression System Vector: PTRC99A
    Mutation: YES
    Organism Common: MALARIAL PARASITE
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833
    Other Details: MUTATION OF V163A PRESENT IN THE WILD TYPE TIM CONSIDERED AS TEMPLATE
    Synonym: TIM, TRIOSE-PHOSPHATE ISOMERASE

 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
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:211 , ASN A:233 , HOH A:2317 , HOH A:2318 , HOH A:2319BINDING SITE FOR RESIDUE SO4 A1249
2AC2SOFTWARESER B:211 , ASN B:233 , HOH B:2336 , HOH B:2337 , HOH B:2338 , HOH B:2339 , HOH B:2340BINDING SITE FOR RESIDUE SO4 B1249

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VFD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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:164-173
B:164-173

(-) Exons   (0, 0)

(no "Exon" information available for 2VFD)

(-) 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:247
 aligned with TPIS_PLAFA | Q07412 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_PLAFA     2 ARKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILAYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
               SCOP domains d2vfda_ A: Triosephosphate isomerase                                                                                                                                                                                                                    SCOP domains
               CATH domains 2vfdA00 A:2-248 Aldolase class I                                                                                                                                                                                                                        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.....eeeehhhhhhhhhhhhhhhh. 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
                 2vfd A   2 ARKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHSERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       


Chain B from PDB  Type:PROTEIN  Length:247
 aligned with TPIS_PLAFA | Q07412 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_PLAFA     2 ARKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILAYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
               SCOP domains d2vfdb_ B: Triosephosphate isomerase                                                                                                                                                                                                                    SCOP domains
               CATH domains 2vfdB00 B:2-248 Aldolase class I                                                                                                                                                                                                                        CATH domains
           Pfam domains (1) ---TIM-2vfdB01 B:5-244                                                                                                                                                                                                                             ---- Pfam domains (1)
           Pfam domains (2) ---TIM-2vfdB02 B:5-244                                                                                                                                                                                                                             ---- Pfam domains (2)
         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: B:4-246 UniProt: 4-246                                                                                                                                                                                                                 -- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------TIM_1      --------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vfd B   2 ARKYFVAANWKCNGTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSYTGEVSAEIAKDLNIEYVIIGHSERRKYFHETDEDVREKLQASLKNNLKAVVCFGESLEQREQNKTIEVITKQVKAFVDLIDNFDNVILVYEPLWAIGTGKTATPEQAQLVHKEIRKIVKDTCGEKQANQIRILYGGSVNTENCSSLIQQEDIDGFLVGNASLKESFVDIIKSAM 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)
(-)
Family: TIM (80)

(-) 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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  TPIS_PLAFA | Q07412
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  5.3.1.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        TPIS_PLAFA | Q07412: 1lyx 1lzo 1m7o 1m7p 1o5x 1vga 1woa 1wob 1ydv 2fi6 2vfe 2vff 2vfg 2vfh 2vfi 3psv 3psw 3pvf 3pwa 3py2 4ywi 4yxg 4z0j 4z0s 4zz9 5bmw 5bmx 5bnk 5brb

(-) Related Entries Specified in the PDB File

1lyx PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE ( PFTIM)-PHOSPHOGLYCOLATE COMPLEX
1lzo PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE- PHOSPHOGLYCOLATE COMPLEX
1m7o PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE ( PFTIM)COMPLED TO SUBSTRATE ANALOG 3- PHOSPHOGLYCERATE (3PG)
1m7p PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE ( PFTIM)COMPLED TO SUBSTRATE ANALOG GLYCEROL-3 -PHOSPHATE (G3P).
1o5x PLASMODIUM FALCIPARUM TIM COMPLEXED TO 2- PHOSPHOGLYCERATE
1vga STRUCTURES OF UNLIGATED AND INHIBITOR COMPLEXES OF W168FMUTANT OF TRIOSEPHOSPHATE ISOMERASE FROM PLASMODIUMFALCIPARUM
1woa STRUCTURE OF THE LOOP6 HINGE MUTANT OF PLASMODIUMFALCIPARUM TRIOSEPHOSPHATE ISOMERASE, W168F, COMPLEXEDWITH GLYCEROL-2-PHOSPHATE
1wob STRUCTURE OF A LOOP6 HINGE MUTANT OF PLASMODIUM FALCIPARUMTRIOSEPHOSPHATE ISOMERASE, W168F, COMPLEXED TO SULFATE
1ydv TRIOSEPHOSPHATE ISOMERASE (TIM)
2vff CRYSTAL STRUCTURE OF THE F96H MUTANT OF PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE
2vfg CRYSTAL STRUCTURE OF THE F96H MUTANT OF PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE WITH 3-PHOSPHOGLYCERATE BOUND AT THE DIMER INTERFACE
2vfh CRYSTAL STRUCTURE OF THE F96W MUTANT OF PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE COMPLEXED WITH 3-PHOSPHOGLYCERATE
2vfi CRYSTAL STRUCTURE OF THE PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE IN THE LOOP CLOSED STATE WITH 3-PHOSPHOGLYCERATE BOUND AT THE ACTIVE SITE AND INTERFACE