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(-) Description

Title :  REFINED CRYSTAL STRUCTURE OF DOGFISH M4 APO-LACTATE DEHYDROGENASE
 
Authors :  J. P. Griffith, M. G. Rossmann
Date :  25 Nov 87  (Deposition) - 12 Jul 89  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Abad-Zapatero, J. P. Griffith, J. L. Sussman, M. G. Rossmann
Refined Crystal Structure Of Dogfish M4 Apo-Lactate Dehydrogenase.
J. Mol. Biol. V. 198 445 1987
PubMed-ID: 3430615  |  Reference-DOI: 10.1016/0022-2836(87)90293-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - M4 LACTATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.27
    Engineered: YES
    Organism Common: SPINY DOGFISH
    Organism Scientific: SQUALUS ACANTHIAS
    Organism Taxid: 7797

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2OXM2Ligand/IonOXAMIC ACID
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2OXM8Ligand/IonOXAMIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:28 , GLY A:29 , ASP A:52 , VAL A:53 , MET A:54 , GLU A:55 , ASP A:56 , LYS A:57 , LEU A:58 , LYS A:59 , GLY A:60 , GLU A:61 , SER A:79 , LYS A:81 , ASP A:82 , TYR A:83 , THR A:95 , ALA A:96 , ALA A:98 , ARG A:99 , VAL A:136 , SER A:137 , ASN A:138 , SER A:161 , HIS A:193 , LEU A:241 , LYS A:242 , TYR A:244 , SER A:246 , OXM A:331 , HOH A:347 , HOH A:353 , HOH A:359 , HOH A:373 , HOH A:384 , HOH A:493 , HOH A:496 , HOH A:497BINDING SITE FOR RESIDUE NAD A 330
2AC2SOFTWAREARG A:106 , HIS A:193 , ALA A:235 , NAD A:330BINDING SITE FOR RESIDUE OXM A 331
3AC3SOFTWAREGLN A:111 , ARG A:171 , HIS A:186 , VAL A:291 , HOH A:335 , HOH A:424 , HOH A:439BINDING SITE FOR RESIDUE OXM A 332

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:138 -Pro A:139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LDHPS00064 L-lactate dehydrogenase active site.LDHA_SQUAC191-197  1A:190-196
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LDHPS00064 L-lactate dehydrogenase active site.LDHA_SQUAC191-197  4A:190-196

(-) Exons   (0, 0)

(no "Exon" information available for 1LDM)

(-) 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:329
 aligned with LDHA_SQUAC | P00341 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:332
                                    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_SQUAC     2 ATLKDKLIGHLATSQEPRSYNKITVVGVGAVGMACAISILMKDLADEVALVDVMEDKLKGEMMDLQHGSLFLHTAKIVSGKDYSVSAGSKLVVITAGARQQEGESRLNLVQRNVNIFKFIIPDIVKHSPDCIILVVSNPVDVLTYVAWKLSGLPMHRIIGSGCNLDSARFRYLMGERLGVHSSSCHGWVIGEHGDSSVPVWSGMNVAGVSLKELHPELGTDKDKENWKKLHKDVVDSAYEVIKLKGYTSWAIGLSVADLAETIMKNLCRVHPVSTMVKDFYGIKNDVFLSLPCVLDNHGISNIVKMKLKPDEEQQLQKSATTLWDIQKDLKF 333
               SCOP domains d1ldma1 A:1-160 Lactate dehydrogenase                                                                                                                           d1ldma2 A:161-329 Lactate dehydrogenase                                                                                                                                      SCOP domains
               CATH domains 1ldmA01 A:1-162 NAD(P)-binding Rossmann-like Domain                                                                                                               1ldmA02 A:163-329 L-2-Hydroxyisocaproate Dehydr   ogenase, subunit A, domain 2                                                                                             CATH domains
               Pfam domains --------------------Ldh_1_N-1ldmA02 A:21-161                                                                                                                     -Ldh_1_C-1ldmA01 A:163-329                      ---                                                                                                                         Pfam domains
         Sec.struct. author .hhhhhhh............eeeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh......eeeee.........eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh....eeeee..............eeee..e---ee............hhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhheeeeeeeeee.........eeeeeeeeeee.eeeeeee.....hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ldm A   1 ATLKDKLIGHLATSQEPRSYNKITVVGVGAVGMACAISILMKDLADEVALVDVMEDKLKGEMMDLQHGSLFLHTAKIVSGKDYSVSAGSKLVVITAGARQQEGESRLNLVQRNVNIFKFIIPNIVKHSPDCIILVVSNPVDVLTYVAWKLSGLPMHRIIGSGCNLDSARFRYLMGERLGVHSCSCHGWVIGEHGDSVPSVWSGMNVASI---KLHPLDGTNKDKQDWKKLHKDVVDSAYEVIKLKGYTSWAIGLSVADLAETIMKNLCRVHPVSTMVKDFYGIKDNVFLSLPCVLNDHGISNIVKMKLKPNEEQQLQKSATTLWDIQKDLKF 329
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        |-  |    217       227       237       247       257       267       277       287       297       307       317       327  
                                                                                                                                                                                                                                          209 210
   Legend:   → Mismatch (orange background)
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  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, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (LDHA_SQUAC | P00341)
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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 Related Entries

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

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        LDHA_SQUAC | P00341: 3ldh 6ldh 8ldh

(-) Related Entries Specified in the PDB File

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