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(-) Description

Title :  A COMPARISON OF THE STRUCTURES OF APO DOGFISH M4 LACTATE DEHYDROGENASE AND ITS TERNARY COMPLEXES
 
Authors :  J. L. White, M. L. Hackert, M. Buehner, M. J. Adams, G. C. Ford, P. J. Lentz I. E. Smiley, S. J. Steindel, M. G. Rossmann
Date :  06 Jun 74  (Deposition) - 29 Apr 77  (Release) - 01 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Oxidoreductase, Choh Donor, Nad Acceptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. White, M. L. Hackert, M. Buehner, M. J. Adams, G. C. Ford, P. J. Lentz Jr. , I. E. Smiley, S. J. Steindel, M. G. Rossmann
A Comparison Of The Structures Of Apo Dogfish M4 Lactate Dehydrogenase And Its Ternary Complexes.
J. Mol. Biol. V. 102 759 1976
PubMed-ID: 940154  |  Reference-DOI: 10.1016/0022-2836(76)90290-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 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  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3PYR1Ligand/IonPYRUVIC ACID
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1ACE4Mod. Amino AcidACETYL GROUP
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3PYR4Ligand/IonPYRUVIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:27 , GLY A:28 , CYS A:29 , ASP A:30 , ASP A:53 , VAL A:54 , MET A:55 , GLU A:56 , ASP A:57 , LYS A:58 , LEU A:59 , LYS A:60 , GLU A:62 , SER A:80 , GLY A:81 , LYS A:83 , ASP A:84 , TYR A:85 , THR A:97 , ALA A:98 , GLY A:99 , ARG A:101 , LEU A:137 , HIS A:138 , PRO A:139 , GLU A:140 , SER A:163 , HIS A:195 , TYR A:246 , ALA A:248 , PYR A:333BINDING SITE FOR RESIDUE NAD A 332
2AC2SOFTWARELEU A:167 , ARG A:171 , HIS A:195 , NAD A:332BINDING SITE FOR RESIDUE PYR A 333

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LDH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LDH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LDH)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LDHPS00064 L-lactate dehydrogenase active site.LDHA_SQUAC191-197  1A:192-198
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LDHPS00064 L-lactate dehydrogenase active site.LDHA_SQUAC191-197  4A:192-198

(-) Exons   (0, 0)

(no "Exon" information available for 3LDH)

(-) 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:330
 aligned with LDHA_SQUAC | P00341 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:352
                                                                                                                                                                                                                                                                                                                                                           303                              
                                                                                                                                                                                                                                                                                        255               256                                           302  |                              
                                    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    |    -         -  |    263       273       283       293        |- |     311       321       331  
          LDHA_SQUAC      1 MATLKDKLIGHLATSQEPRSYNKITVVGVGAVGMACAISILMKDLADEVALVDVMEDKLKGEMMDLQHGSLFLHTAKIVSGKDYSVSAGSKLVVITAGARQQEGESRLNLVQRNVNIFKFIIPDIVKHSPDCIILVVSNPVDVLTYVAWKLSGLPMHRIIGSGCNLDSARFRYLMGERLGVHSSSCHGWVIGEHGDSSVPVWSGMNVAGVSLKELHPELGTDKDKENWKKLHKDVVDSAYEVIKLKGYTSWAIGL-----------------SVADLAETIMKNLCRVHPVSTMVKDFYGIKNDVFLSLPCVLDNHGIS--NIVKMKLKPDEEQQLQKSATTLWDIQKDLKF  333
               SCOP domains d3ldha_ A: Lactate dehydrogenase                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -3ldhA01 A:1-164 NAD(P)-binding Rossmann-like Domain                                                                                                               3ldhA02 A:165-331 L-2-Hydroxyisocaproate Dehy                     drogenase, subunit A, domain 2                                                                                              CATH domains
               Pfam domains ---------------------Ldh_1_N-3ldhA02 A:22-163                                                                                                                     -Ldh_1_C-3ldhA01 A:165-330                                                                                                                                                                   - Pfam domains
         Sec.struct. author ..hhhhhhh............eeeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh......eeeee.........eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh....eeeee..............eeee.---------------------.eee............hhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhheeeeeeeeee.........eeeeeeeeeee-.eeeeeee.....hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ldh A    0 xTALKDKLIGHLATSQEPRSYNKITVVGCDAVGMADAISVLMKDLADEVALVDVMEDKLKGEMMDLEHGSLFLHTAKIVSGKDYSVSAGSKLVVITAGARQQEGESRLNLVQRNVNIFKFIIPNIVKHSPDCLKELHPELGTDKNKQDWKLSGLPMHRIIGSGCNLDSARFRYLMGERLGVHSCLVIGWVIGQHGDSVPSVWSGMWDA---------------------KLHKDVVDSAYEVIKLKGYTSWAIGLVVSNPVDVLTYVAWKGCSVADLAQTIMKDLCRVHPVSTMVKDFYGIKDNVFLSLPCVLNN-GISHCNIVKMKLKPDEEQQLQKSATTLWDIQKDLKF  331
                            |        9        19||      30        40        50        60        70        80||      91       101 ||    112       122      132A|      141       151       161       171       181       191       201       | -         -       210       220       230       240       250       260       270       280       290    | |299       309       319       329  
                            |                  20|                                                         81|                 103|                       132A|                                                                          209                   210                                                                                  295 |                                   
                            0-ACE               22                                                          83                  105                        132B                                                                                                                                                                                       296
   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  (1, 1)

Asymmetric Unit
(-)
Class: Low resolution protein structures (283)

(-) 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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        LDHA_SQUAC | P00341: 1ldm 6ldh 8ldh

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