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(-) Description

Title :  TOXOPLASMA GONDII BRADYZOITE-SPECIFIC LDH (LDH2) APO FORM
 
Authors :  K. L. Kavanagh, D. K. Wilson
Date :  15 Mar 04  (Deposition) - 15 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Rossmann Fold, Tetramer, Nad-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. L. Kavanagh, D. K. Wilson
Structure Of Apo And Ternary Forms Of Toxoplasma Gondii Ldh
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - L-LACTATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB12
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: TOXOPLASMA GONDII
    Organism Taxid: 5811
    Synonym: LDH, LDH2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1SOV)

(-) Sites  (0, 0)

(no "Site" information available for 1SOV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:140 -Pro A:141
2Asn B:140 -Pro B:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SOV)

(-) Exons   (0, 0)

(no "Exon" information available for 1SOV)

(-) 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:316
 aligned with LDH_TOXGO | Q27797 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:323
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322   
           LDH_TOXGO      3 GTVSRRKKIAMIGSGMIGGTMGYLCVLRELADVVLFDVVTGMPEGKALDDSQATSIADTNVSVTSANQYEKIAGSDVVIITAGLTKVPGKSDKEWSRNDLLPFNAKIIREVAQGVKKYCPLAFVIVVTNPLDCMVKCFHEASGLPKNMVCGMANVLDSARFRRFIADQLEISPRDIQATVIGTHGDHMLPLARYVTVSGFPLREFIKKGKMTEAKLAEIVERTKKAGGEIVRLLGQGSAYYAPALSAITMAQAFLKDEKRVLPCSVYCQGEYGLHDMFIGLPAVIGGGGIEQVIELELTHEEQECFRKSVDDVVELNKSLAAL  325
               SCOP domains d1sova1 A:15-163 automated matches                                                                                                                      d1sova2 A:164-331 automated matches                                                                                                                                         SCOP domains
               CATH domains 1sovA01 A:15-162 NAD(P)-binding Rossmann-like Domain                                                                                                   1sovA02 A:163-331 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee........-------hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee..hhhhhee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...ee..eeeeee.hhh.eeeeeee.eeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1sov A   15 GTVSRRKKIAMIGSGMIGGTMGYLCVLRELADVVLFDVVTGMPEGKALDDSQATSIADTNVSVTSANQYEKIAGSDVVIITAGLTKVP-------SRNDLLPFNAKIIREVAQGVKKYCPLAFVIVVTNPLDCMVKCFHEASGLPKNMVCGMANVLDSARFRRFIADQLEISPRDIQATVIGTHGDHMLPLARYVTVNGFPLREFIKKGKMTEAKLAEIVERTKKAGGEIVRLLGQGSAYYAPALSAITMAQAFLKDEKRVLPCSVYCQGEYGLHDMFIGLPAVIGGGGIEQVIELELTHEEQECFRKSVDDVVELNKSLAAL  331
                                    24        35        45 ||     56        66      ||75     || 86        96      || -     | 112       122      132A|      141       151       161       171       181       191       201      209C|||    218    || 229       239  |||  247       257       267       277     ||288       298||     309       319     ||328   
                                             33|          47|                     73A|      81|                103A|     108                    132A|                                                                         209A|||||   216|  223|             242A||                                      283|           299|                    325A|      
                                              35           49                      73B       83                 103B                             132B                                                                          209B||||    218   225              242B|                                       285            301                     325B      
                                                                                                                                                                                                                                209C|||                            242C                                                                                        
                                                                                                                                                                                                                                 209D||                                                                                                                        
                                                                                                                                                                                                                                  210A|                                                                                                                        
                                                                                                                                                                                                                                   210B                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:315
 aligned with LDH_TOXGO | Q27797 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:323
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322   
           LDH_TOXGO      3 GTVSRRKKIAMIGSGMIGGTMGYLCVLRELADVVLFDVVTGMPEGKALDDSQATSIADTNVSVTSANQYEKIAGSDVVIITAGLTKVPGKSDKEWSRNDLLPFNAKIIREVAQGVKKYCPLAFVIVVTNPLDCMVKCFHEASGLPKNMVCGMANVLDSARFRRFIADQLEISPRDIQATVIGTHGDHMLPLARYVTVSGFPLREFIKKGKMTEAKLAEIVERTKKAGGEIVRLLGQGSAYYAPALSAITMAQAFLKDEKRVLPCSVYCQGEYGLHDMFIGLPAVIGGGGIEQVIELELTHEEQECFRKSVDDVVELNKSLAAL  325
               SCOP domains d1sovb1 B:15-163 automated matches                                                                                                                      d1sovb2 B:164-331 automated matches                                                                                                                                         SCOP domains
               CATH domains 1sovB01 B:15-162 NAD(P)-binding Rossmann-like Domain                                                                                                   1sovB02 B:163-331 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                  CATH domains
           Pfam domains (1) ------Ldh_1_N-1sovB03 B:21-163                                                                                                                          -Ldh_1_C-1sovB01 B:165-330                                                                                                                                                - Pfam domains (1)
           Pfam domains (2) ------Ldh_1_N-1sovB04 B:21-163                                                                                                                          -Ldh_1_C-1sovB02 B:165-330                                                                                                                                                - Pfam domains (2)
         Sec.struct. author .......eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee.......--------hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee..hhhhhee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...ee..eeeeee.hhh.eeeeeee.eeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1sov B   15 GTVSRRKKIAMIGSGMIGGTMGYLCVLRELADVVLFDVVTGMPEGKALDDSQATSIADTNVSVTSANQYEKIAGSDVVIITAGLTKV--------SRNDLLPFNAKIIREVAQGVKKYCPLAFVIVVTNPLDCMVKCFHEASGLPKNMVCGMANVLDSARFRRFIADQLEISPRDIQATVIGTHGDHMLPLARYVTVNGFPLREFIKKGKMTEAKLAEIVERTKKAGGEIVRLLGQGSAYYAPALSAITMAQAFLKDEKRVLPCSVYCQGEYGLHDMFIGLPAVIGGGGIEQVIELELTHEEQECFRKSVDDVVELNKSLAAL  331
                                    24        35        45 ||     56        66      ||75     || 86        96      |  -     | 112       122      132A|      141       151       161       171       181       191       201      209C|||    218    || 229       239  |||  247       257       267       277     ||288       298||     309       319     ||328   
                                             33|          47|                     73A|      81|                103A      108                    132A|                                                                         209A|||||   216|  223|             242A||                                      283|           299|                    325A|      
                                              35           49                      73B       83                                                  132B                                                                          209B||||    218   225              242B|                                       285            301                     325B      
                                                                                                                                                                                                                                209C|||                            242C                                                                                        
                                                                                                                                                                                                                                 209D||                                                                                                                        
                                                                                                                                                                                                                                  210A|                                                                                                                        
                                                                                                                                                                                                                                   210B
   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: LDH_C (56)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LDH_TOXGO | Q27797)
molecular function
    GO:0004459    L-lactate dehydrogenase activity    Catalysis of the reaction: (S)-lactate + NAD+ = pyruvate + NADH + H+.
    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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0019752    carboxylic acid metabolic process    The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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    Asn A:140 - Pro A:141   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        LDH_TOXGO | Q27797: 1sow 3czm

(-) Related Entries Specified in the PDB File

1sow