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(-) Description

Title :  CHARACTERIZATION OF THE ANTIGENIC SITES ON THE REFINED 3-ANGSTROMS RESOLUTION STRUCTURE OF MOUSE TESTICULAR LACTATE DEHYDROGENASE C4
 
Authors :  J. P. Griffith, M. G. Rossmann
Date :  25 Nov 87  (Deposition) - 19 Apr 89  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.96
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase(Choh(D)-Nad(A)) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. H. Hogrefe, J. P. Griffith, M. G. Rossmann, E. Goldberg
Characterization Of The Antigenic Sites On The Refined 3-A Resolution Structure Of Mouse Testicular Lactate Dehydrogenase C4.
J. Biol. Chem. V. 262 13155 1987
PubMed-ID: 2443489
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - APO-LACTATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.27
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2LDX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:137 -Pro A:138
2Asn B:137 -Pro B:138
3Asn C:137 -Pro C:138
4Asn D:137 -Pro D:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LDHPS00064 L-lactate dehydrogenase active site.LDHC_MOUSE190-196
 
 
 		  4A:189-195
B:189-195
C:189-195
D:189-195

(-) Exons   (0, 0)

(no "Exon" information available for 2LDX)

(-) 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:331
 aligned with LDHC_MOUSE | P00342 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:331
                                    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 
           LDHC_MOUSE     2 STVKEQLIQNLVPEDKLSRCKITVVGVGNVGMACAISILLKGLADELALVDADTNKLRGEALDLLHGSLFLSTPKIVFGKDYNVSANSKLVIITAGARMVSGETRLDLLQRNVAIMKAIVPGIVQNSPDCKIIIVTNPVDILTYVVWKISGFPVGRVIGSGCNLDSARFRYLIGEKLGVNPTSCHGWVLGEHGDSSVPIWSGVNVAGVTLKSLNPAIGTDSDKEHWKNVHKQVVEGGYEVLNMKGYTSWAIGLSVTDLARSILKNLKRVHPVTTLVKGFHGIKEEVFLSIPCVLGQSGITDFVKVNMTAEEEGLLKKSADTLWNMQKDLQL 332
               SCOP domains d2ldxa1 A:1-159 Lactate dehydrogenase                                                                                                                          d2ldxa2 A:160-331 Lactate dehydrogenase                                                                                                                                      SCOP domains
               CATH domains 2ldxA01 A:1-161 NAD(P)-binding Rossmann-like Domain                                                                                                              2ldxA02 A:162-331 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh............eeeee..hhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhh.......eeeee........eeeeee...............hhhhhhhhhhhh.hhhhhh...eeee...hhhhhhhhhhhhhh.....eee..hhhhhhhhhhhhhhhhh.........eee.....eee...........................hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ldx A   1 STVKEQLIQNLVPEDKLSRCKITVVGVGDVGMACAISILLKGLADELALVDADTDKLRGEALDLQHGSLFLSTPKIVFGKDYNVSANSKLVIITAGARMVSGQTRLDLLQRNVAIMKAIVPGVIQNSPDCKIIVVTNPVDILTYVVWKISGFPVGRVIGSGCNLDSARFRYLIGEKLGVNPTSCHGWVLGEHGDSSVPIWSGVNVAGVTLKSLNPAIGTDKNKQHWKNVHKQVVEGGYEVLDMKGYTSWAIGLSVTDLARSILKNLKRVHPVTTLVKGFHGIKEEVFLSIPCVLGESGITDFVKVNMTAEEEGLLKKSADTLWNMQKNLEL 331
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330 


Chain B from PDB  Type:PROTEIN  Length:331
 aligned with LDHC_MOUSE | P00342 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:331
                                    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 
           LDHC_MOUSE     2 STVKEQLIQNLVPEDKLSRCKITVVGVGNVGMACAISILLKGLADELALVDADTNKLRGEALDLLHGSLFLSTPKIVFGKDYNVSANSKLVIITAGARMVSGETRLDLLQRNVAIMKAIVPGIVQNSPDCKIIIVTNPVDILTYVVWKISGFPVGRVIGSGCNLDSARFRYLIGEKLGVNPTSCHGWVLGEHGDSSVPIWSGVNVAGVTLKSLNPAIGTDSDKEHWKNVHKQVVEGGYEVLNMKGYTSWAIGLSVTDLARSILKNLKRVHPVTTLVKGFHGIKEEVFLSIPCVLGQSGITDFVKVNMTAEEEGLLKKSADTLWNMQKDLQL 332
               SCOP domains d2ldxb1 B:1-159 Lactate dehydrogenase                                                                                                                          d2ldxb2 B:160-331 Lactate dehydrogenase                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh............eeeee..hhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhh.......eeeee........eeeeee...............hhhhhhhhhhhh.hhhhhh...eeee...hhhhhhhhhhhhhh.....eee..hhhhhhhhhhhhhhhhh.........eee.....eee...........................hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ldx B   1 STVKEQLIQNLVPEDKLSRCKITVVGVGDVGMACAISILLKGLADELALVDADTDKLRGEALDLQHGSLFLSTPKIVFGKDYNVSANSKLVIITAGARMVSGQTRLDLLQRNVAIMKAIVPGVIQNSPDCKIIVVTNPVDILTYVVWKISGFPVGRVIGSGCNLDSARFRYLIGEKLGVNPTSCHGWVLGEHGDSSVPIWSGVNVAGVTLKSLNPAIGTDKNKQHWKNVHKQVVEGGYEVLDMKGYTSWAIGLSVTDLARSILKNLKRVHPVTTLVKGFHGIKEEVFLSIPCVLGESGITDFVKVNMTAEEEGLLKKSADTLWNMQKNLEL 331
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330 


Chain C from PDB  Type:PROTEIN  Length:331
 aligned with LDHC_MOUSE | P00342 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:331
                                    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 
           LDHC_MOUSE     2 STVKEQLIQNLVPEDKLSRCKITVVGVGNVGMACAISILLKGLADELALVDADTNKLRGEALDLLHGSLFLSTPKIVFGKDYNVSANSKLVIITAGARMVSGETRLDLLQRNVAIMKAIVPGIVQNSPDCKIIIVTNPVDILTYVVWKISGFPVGRVIGSGCNLDSARFRYLIGEKLGVNPTSCHGWVLGEHGDSSVPIWSGVNVAGVTLKSLNPAIGTDSDKEHWKNVHKQVVEGGYEVLNMKGYTSWAIGLSVTDLARSILKNLKRVHPVTTLVKGFHGIKEEVFLSIPCVLGQSGITDFVKVNMTAEEEGLLKKSADTLWNMQKDLQL 332
               SCOP domains d2ldxc1 C:1-159 Lactate dehydrogenase                                                                                                                          d2ldxc2 C:160-331 Lactate dehydrogenase                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh............eeeee..hhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhh.......eeeee........eeeeee...............hhhhhhhhhhhh.hhhhhh...eeee...hhhhhhhhhhhhhh.....eee..hhhhhhhhhhhhhhhhh.........eee.....eee...........................hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ldx C   1 STVKEQLIQNLVPEDKLSRCKITVVGVGDVGMACAISILLKGLADELALVDADTDKLRGEALDLQHGSLFLSTPKIVFGKDYNVSANSKLVIITAGARMVSGQTRLDLLQRNVAIMKAIVPGVIQNSPDCKIIVVTNPVDILTYVVWKISGFPVGRVIGSGCNLDSARFRYLIGEKLGVNPTSCHGWVLGEHGDSSVPIWSGVNVAGVTLKSLNPAIGTDKNKQHWKNVHKQVVEGGYEVLDMKGYTSWAIGLSVTDLARSILKNLKRVHPVTTLVKGFHGIKEEVFLSIPCVLGESGITDFVKVNMTAEEEGLLKKSADTLWNMQKNLEL 331
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330 


Chain D from PDB  Type:PROTEIN  Length:331
 aligned with LDHC_MOUSE | P00342 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:331
                                    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 
           LDHC_MOUSE     2 STVKEQLIQNLVPEDKLSRCKITVVGVGNVGMACAISILLKGLADELALVDADTNKLRGEALDLLHGSLFLSTPKIVFGKDYNVSANSKLVIITAGARMVSGETRLDLLQRNVAIMKAIVPGIVQNSPDCKIIIVTNPVDILTYVVWKISGFPVGRVIGSGCNLDSARFRYLIGEKLGVNPTSCHGWVLGEHGDSSVPIWSGVNVAGVTLKSLNPAIGTDSDKEHWKNVHKQVVEGGYEVLNMKGYTSWAIGLSVTDLARSILKNLKRVHPVTTLVKGFHGIKEEVFLSIPCVLGQSGITDFVKVNMTAEEEGLLKKSADTLWNMQKDLQL 332
               SCOP domains d2ldxd1 D:1-159 Lactate dehydrogenase                                                                                                                          d2ldxd2 D:160-331 Lactate dehydrogenase                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------Ldh_1_N-2ldxD05 D:20-160                                                                                                                     -Ldh_1_C-2ldxD01 D:162-327                                                                                                                                             ---- Pfam domains (1)
           Pfam domains (2) -------------------Ldh_1_N-2ldxD06 D:20-160                                                                                                                     -Ldh_1_C-2ldxD02 D:162-327                                                                                                                                             ---- Pfam domains (2)
           Pfam domains (3) -------------------Ldh_1_N-2ldxD07 D:20-160                                                                                                                     -Ldh_1_C-2ldxD03 D:162-327                                                                                                                                             ---- Pfam domains (3)
           Pfam domains (4) -------------------Ldh_1_N-2ldxD08 D:20-160                                                                                                                     -Ldh_1_C-2ldxD04 D:162-327                                                                                                                                             ---- Pfam domains (4)
         Sec.struct. author .hhhhhhh............eeeee..hhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhh.......eeeee........eeeeee...............hhhhhhhhhhhh.hhhhhh...eeee...hhhhhhhhhhhhhh.....eee............................eee.....eee...........................hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ldx D   1 STVKEQLIQNLVPEDKLSRCKITVVGVGDVGMACAISILLKGLADELALVDADTDKLRGEALDLQHGSLFLSTPKIVFGKDYNVSANSKLVIITAGARMVSGQTRLDLLQRNVAIMKAIVPGVIQNSPDCKIIVVTNPVDILTYVVWKISGFPVGRVIGSGCNLDSARFRYLIGEKLGVNPTSCHGWVLGEHGDSSVPIWSGVNVAGVTLKSLNPAIGTDKNKQHWKNVHKQVVEGGYEVLDMKGYTSWAIGLSVTDLARSILKNLKRVHPVTTLVKGFHGIKEEVFLSIPCVLGESGITDFVKVNMTAEEEGLLKKSADTLWNMQKNLEL 331
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330
   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, 8)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Clan: LDH_C (56)
(-)
Family: Ldh_1_C (51)
(-)
Mus musculus (Mouse) (1)
1aLdh_1_C-2ldxD01D:162-327
1bLdh_1_C-2ldxD02D:162-327
1cLdh_1_C-2ldxD03D:162-327
1dLdh_1_C-2ldxD04D:162-327
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (LDHC_MOUSE | P00342)
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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006754    ATP biosynthetic process    The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0030317    flagellated sperm motility    Any process involved in the controlled movement of a flagellated sperm cell.
    GO:0019244    lactate biosynthetic process from pyruvate    The chemical reactions and pathways resulting in the formation of lactate from other compounds, including pyruvate.
    GO:0019516    lactate oxidation    The chemical reactions and pathways resulting in the conversion of lactate to other compounds, such as pyruvate, with concomitant loss of electrons.
    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.
    GO:0006090    pyruvate metabolic process    The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.
cellular component
    GO:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0031514    motile cilium    A cilium which may have a variable arrangement of axonemal microtubules and also contains molecular motors. It may beat with a whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface, such as on epithelial cells that line the lumenal ducts of various tissues; or they may display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization. Motile cilia can be found in single as well as multiple copies per cell.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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