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(-) Description

Title :  CRYSTAL STRUCTURE OF F16BP ALDOLASE FROM TOXOPLASMA GONDII (TGALD1)
 
Authors :  M. L. Tonkin, R. Ramaswamy, A. S. Halavaty, J. Ruan, M. Igarashi, H. M. Ng M. J. Boulanger
Date :  09 May 14  (Deposition) - 15 Oct 14  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Lyase, Apicomplexa, Tim Barrel, Glycolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. L. Tonkin, A. S. Halavaty, R. Ramaswamy, J. Ruan, M. Igarashi, H. M. Ngo, M. J. Boulanger
Structural And Functional Divergence Of The Aldolase Fold In Toxoplasma Gondii.
J. Mol. Biol. V. 427 840 2015
PubMed-ID: 25284756  |  Reference-DOI: 10.1016/J.JMB.2014.09.019

(-) Compounds

Molecule 1 - FRUCTOSE-BISPHOSPHATE ALDOLASE
    Chains: A
    EC Number: 4.1.2.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET28A MODIFIED
    Expression System Vector Type: PLASMID
    Fragment: F16BP ALDOLASE, RESIDUES 7-422
    Organism Scientific: TOXOPLASMA GONDII
    Organism Taxid: 5811
    Synonym: ALDOLASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3GOL1Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (4, 24)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
2BME4Ligand/IonBETA-MERCAPTOETHANOL
3GOL4Ligand/IonGLYCEROL
4SO48Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:267 , ASP A:269 , HIS A:307 , CYS A:311 , HOH A:2145BINDING SITE FOR RESIDUE BME A1422
2AC2SOFTWAREASP A:104 , SER A:106 , THR A:109 , LYS A:177 , HOH A:2044BINDING SITE FOR RESIDUE SO4 A1417
3AC3SOFTWAREARG A:113 , GLY A:373 , ARG A:374 , HOH A:2138 , HOH A:2158 , HOH A:2160BINDING SITE FOR RESIDUE SO4 A1418
4AC4SOFTWARELYS A:177 , VAL A:178 , ASP A:179 , ARG A:203 , TYR A:207BINDING SITE FOR RESIDUE ACT A1419
5AC5SOFTWARETHR A:184 , SER A:201BINDING SITE FOR RESIDUE ACT A1420
6AC6SOFTWAREASN A:121 , GLU A:123BINDING SITE FOR RESIDUE GOL A1421

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D2J)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:229 -Pro A:230
2Gly A:362 -Pro A:363

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D2J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D2J)

(-) Exons   (0, 0)

(no "Exon" information available for 4D2J)

(-) Sequences/Alignments

Asymmetric 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:338
 aligned with B9PW35_TOXGV | B9PW35 from UniProtKB/TrEMBL  Length:433

    Alignment length:338
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408        
         B9PW35_TOXGV    79 SQEVAKELAENARKIAAPGKGILAADESTGTIKKRFDSIGVENTEANRAFYRDLLFSTKGLGQYISGAILFEETLYQKSPSGVPMVDLLKAEGIIPGIKVDKGLETLPLTDDEKATMGLDGLSERCKKYYEAGARFAKWRAVLSIDPAKGKPTNLSITEVAHGLARYAAICQANRLVPIVEPEILTDGSHDITVCAEVTERVLAAVFKALNDHHVLLEGALLKPNMVTHGSDCPKPASHEEIAFYTVRSLKRTVPPALPGVMFLSGGQSEEDASLNLNEMNKMGPHPFQLSFSYGRALQASCLKAWKGVPENKAKAQQVLMERARANGEAQLGKYGGG 416
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhh.eeeeeehhhhhh.......hhhhhhhhh..eeeee....eee.......eee....hhhhhhhhhhhh...eeeeeeee...hhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhee...............hhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d2j A  79 SQEVAKELAENARKIAAPGKGILAADESTGTIKKRFDSIGVENTEANRAFYRDLLFSTKGLGQYISGAILFEETLYQKSPSGVPMVDLLKAEGIIPGIKVDKGLETLPLTDDEKATMGLDGLSERCKKYYEAGARFAKWRAVLSIDPAKGKPTNLSITEVAHGLARYAAICQANRLVPIVEPEILTDGSHDITVCAEVTERVLAAVFKALNDHHVLLEGALLKPNMVTHGSDCPKPASHEEIAFYTVRSLKRTVPPALPGVMFLSGGQSEEDASLNLNEMNKMGPHPFQLSFSYGRALQASCLKAWKGVPENKAKAQQVLMERARANGEAQLGKYGGG 416
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4D2J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D2J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D2J)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (B9PW35_TOXGV | B9PW35)
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:0004332    fructose-bisphosphate aldolase activity    Catalysis of the reaction: D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde-3-phosphate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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        B9PW35_TOXGV | B9PW35: 4tu1

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