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(-) Description

Title :  APO LDH FROM THE PSYCHROPHILE C. GUNNARI
 
Authors :  N. Coquelle, D. Madern, F. Vellieux
Date :  13 Jul 07  (Deposition) - 25 Sep 07  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  B  (4x)
Keywords :  Oxidoreductase, Lactate Dehydrogenase, Nad, Fish, Glycolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Coquelle, E. Fioravanti, M. Weik, F. Vellieux, D. Madern
Activity, Stability And Structural Studies Of Lactate Dehydrogenases Adapted To Extreme Thermal Environments.
J. Mol. Biol. V. 374 547 2007
PubMed-ID: 17936781  |  Reference-DOI: 10.1016/J.JMB.2007.09.049

(-) Compounds

Molecule 1 - L-LACTATE DEHYDROGENASE A CHAIN
    ChainsA, B
    EC Number1.1.1.27
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-11A
    Expression System StrainBL21(DE3)-RIL
    Expression System Taxid469008
    Organism CommonMACKEREL ICEFISH
    Organism ScientificCHAMPSOCEPHALUS GUNNARI
    Organism Taxid52237
    SynonymLDH-A
    TissueMUSCLE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (4x)A 
Biological Unit 2 (4x) B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2V65)

(-) Sites  (0, 0)

(no "Site" information available for 2V65)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V65)

(-) 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 2V65)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LDHPS00064 L-lactate dehydrogenase active site.LDHA_CHAGU189-195
 
  2A:192-198
B:192-198
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LDHPS00064 L-lactate dehydrogenase active site.LDHA_CHAGU189-195
 
  4A:192-198
-
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LDHPS00064 L-lactate dehydrogenase active site.LDHA_CHAGU189-195
 
  4-
B:192-198

(-) Exons   (0, 0)

(no "Exon" information available for 2V65)

(-) 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:326
 aligned with LDHA_CHAGU | O93541 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:330
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331
          LDHA_CHAGU      2 STKEKLISHVMKEEPVGSRSKVTVVGVGMVGMASAISILLKDLCDELAMVDVMEDKLKGEVMDLQHGSLFLKTKIVGDKDYSVTANSKVVVVTAGARQQEGESRLNLVQRNVNIFKFIIPNIVKYSPNCILMVVSNPVDILTYVAWKLSGFPRHRVIGSGTNLDSARFRHLIGEKLHLHPSSCHAWIVGEHGDSSVPVWSGVNVAGVSLQGLNPQMGTEGDGENWKAIHKEVVDGAYEVIKLKGYTSWAIGMSVADLVESIIKNMHKVHPVSTLVQGMHGVKDEVFLSVPCVLGNSGLTDVIHMTLKAEEEKQLQKSAETLWGVQKELTL  331
               SCOP domains d2v65a1 A:2-162 automated matches                                                                                                                             d2v65a2 A:163-331 automated matches                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhh..............eeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh..eeee..hhhhhh...eeee....----..hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhh...hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhhhee...................hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2v65 A    2 STKEKLISHVMKEEPVGSRSKVTVVGVGMVGMASAISILLKDLCDELAMVDVMEDKLKGEVMDLQHGSLFLKTKIVGDKDYSVTANSKVVVVTAGA----GESRLNLVQRNVNIFKFIIPNIVKYSPNCILMVVSNPVDILTYVAWKLSGFPRHRVIGSGTNLDSARFRHLIGEKLHLHPSSCHAWIVGEHGDSSVPVWSGVNVAGVSLQGLNPQMGTEGDGENWKAIHKEVVDGAYEVIKLKGYTSWAIGMSVADLVESIIKNMHKVHPVSTLVQGMHGVKDEVFLSVPCVLGNSGLTDVIHMTLKAEEEKQLQKSAETLWGVQKELTL  331
                                    11        22        32        42        52        62        72       |84        94     |   -|      115       125      |134       144       154       164       174       184       194       204    ||210B       220       230       240       250       260       270       280       290       301       311       321       331
                                             20|                                                        80|              100  106                      132A|                                                                         209A|||||                                                                                      299|                              
                                              22                                                         83                                             132B                                                                          209B||||                                                                                       301                              
                                                                                                                                                                                                                                       209C|||                                                                                                                        
                                                                                                                                                                                                                                        209D||                                                                                                                        
                                                                                                                                                                                                                                         210A|                                                                                                                        
                                                                                                                                                                                                                                          210B                                                                                                                        

Chain B from PDB  Type:PROTEIN  Length:325
 aligned with LDHA_CHAGU | O93541 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:330
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331
          LDHA_CHAGU      2 STKEKLISHVMKEEPVGSRSKVTVVGVGMVGMASAISILLKDLCDELAMVDVMEDKLKGEVMDLQHGSLFLKTKIVGDKDYSVTANSKVVVVTAGARQQEGESRLNLVQRNVNIFKFIIPNIVKYSPNCILMVVSNPVDILTYVAWKLSGFPRHRVIGSGTNLDSARFRHLIGEKLHLHPSSCHAWIVGEHGDSSVPVWSGVNVAGVSLQGLNPQMGTEGDGENWKAIHKEVVDGAYEVIKLKGYTSWAIGMSVADLVESIIKNMHKVHPVSTLVQGMHGVKDEVFLSVPCVLGNSGLTDVIHMTLKAEEEKQLQKSAETLWGVQKELTL  331
               SCOP domains d2v65b1 B:2-162 automated matches                                                                                                                             d2v65b2 B:163-331 automated matches                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------------------Ldh_1_N-2v65B03 B:22-163                                                                                                                    -Ldh_1_C-2v65B01 B:165-329                                                                                                                                               -- Pfam domains (1)
           Pfam domains (2) -------------------Ldh_1_N-2v65B04 B:22-163                                                                                                                    -Ldh_1_C-2v65B02 B:165-329                                                                                                                                               -- Pfam domains (2)
         Sec.struct. author hhhhhhh..............eeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh..eeee..hhhhhh...eeee....-----.hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhhhee...................hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2v65 B    2 STKEKLISHVMKEEPVGSRSKVTVVGVGMVGMASAISILLKDLCDELAMVDVMEDKLKGEVMDLQHGSLFLKTKIVGDKDYSVTANSKVVVVTAGA-----ESRLNLVQRNVNIFKFIIPNIVKYSPNCILMVVSNPVDILTYVAWKLSGFPRHRVIGSGTNLDSARFRHLIGEKLHLHPSSCHAWIVGEHGDSSVPVWSGVNVAGVSLQGLNPQMGTEGDGENWKAIHKEVVDGAYEVIKLKGYTSWAIGMSVADLVESIIKNMHKVHPVSTLVQGMHGVKDEVFLSVPCVLGNSGLTDVIHMTLKAEEEKQLQKSAETLWGVQKELTL  331
                                    11        22        32        42        52        62        72       |84        94     |   - |     115       125      |134       144       154       164       174       184       194       204    ||210B       220       230       240       250       260       270       280       290       301       311       321       331
                                             20|                                                        80|              100   107                     132A|                                                                         209A|||||                                                                                      299|                              
                                              22                                                         83                                             132B                                                                          209B||||                                                                                       301                              
                                                                                                                                                                                                                                       209C|||                                                                                                                        
                                                                                                                                                                                                                                        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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V65)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: LDH_C (56)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LDHA_CHAGU | O93541)
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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    Asn A:140 - Pro A:141   [ RasMol ]  
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(-) Related Entries Specified in the PDB File

2v6b LACTATE DEHYDROGENASE APO FORM