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(-) Description

Title :  CRYSTAL STRUCTURE OF LACTATE DEHYDROGENASE FROM STAPHYLOCOCCUS AUREUS COMPLEXED WITH NAD AND PYRUVATE
 
Authors :  V. L. Schramm, S. C. Almo, J. A. Gutierrez, M. Ho
Date :  14 May 08  (Deposition) - 02 Jun 09  (Release) - 02 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  B  (2x)
Keywords :  Lactate Dehydrogenase, Staphylococcus Aureus, Nad, Pyruvate, Cytoplasm, Glycolysis, Oxidoreductase, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. L. Schramm, S. C. Almo, J. A. Gutierrez, M. Ho
Crystal Structure Of Lactate Dehydrogenase From Staphylococcus Aureus Complexed With Nad And Pyruvate
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-LACTATE DEHYDROGENASE 1
    ChainsA, B
    EC Number1.1.1.27
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneLDH1, SACOL0222
    Organism ScientificSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS COL
    Organism Taxid93062
    SynonymL-LDH 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB
Biological Unit 2 (2x)A 
Biological Unit 3 (2x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2PYR2Ligand/IonPYRUVIC ACID
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2PYR4Ligand/IonPYRUVIC ACID
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2PYR2Ligand/IonPYRUVIC ACID
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2PYR2Ligand/IonPYRUVIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:15 , ALA A:16 , ASP A:38 , LEU A:39 , CYS A:81 , ALA A:82 , GLY A:83 , ALA A:84 , ALA A:122 , THR A:123 , ASN A:124 , SER A:147 , LEU A:151 , HIS A:179 , THR A:232BINDING SITE FOR RESIDUE NAD A 318
2AC2SOFTWAREASN A:124 , LEU A:151 , ARG A:155 , HIS A:179 , ALA A:222 , THR A:232BINDING SITE FOR RESIDUE PYR A 319
3AC3SOFTWAREGLY B:15 , ALA B:16 , ASP B:38 , LEU B:39 , CYS B:81 , ALA B:82 , GLY B:83 , ALA B:84 , ALA B:122 , THR B:123 , ASN B:124 , SER B:147 , LEU B:151 , HIS B:179 , THR B:232BINDING SITE FOR RESIDUE NAD B 318
4AC4SOFTWAREASN B:124 , LEU B:151 , ARG B:155 , HIS B:179 , ALA B:222 , THR B:232BINDING SITE FOR RESIDUE PYR B 319

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D4P)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:124 -Pro A:125
2Asn B:124 -Pro B:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D4P)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LDHPS00064 L-lactate dehydrogenase active site.LDH1_STAAC176-182
 
  2A:176-182
B:176-182
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LDHPS00064 L-lactate dehydrogenase active site.LDH1_STAAC176-182
 
  4A:176-182
B:176-182
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LDHPS00064 L-lactate dehydrogenase active site.LDH1_STAAC176-182
 
  2A:176-182
-
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LDHPS00064 L-lactate dehydrogenase active site.LDH1_STAAC176-182
 
  2-
B:176-182

(-) Exons   (0, 0)

(no "Exon" information available for 3D4P)

(-) 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:307
 aligned with LDH1_STAAC | Q5HJD7 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:309
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303         
           LDH1_STAAC     4 FKGNKVVLIGNGAVGSSYAFSLVNQSIVDELVIIDLDTEKVRGDVMDLKHATPYSPTTVRVKAGEYSDCHDADLVVICAGAAQKPGETRLDLVSKNLKIFKSIVGEVMASKFDGIFLVATNPVDILAYATWKFSGLPKERVIGSGTILDSARFRLLLSEAFDVAPRSVDAQIIGEHGDTELPVWSHANIAGQPLKTLLEQRPEGKAQIEQIFVQTRDAAYDIIQAKGATYYGVAMGLARITEAIFRNEDAVLTVSALLEGEYEEEDVYIGVPAVINRNGIRNVVEIPLNDEEQSKFAHSAKTLKDIMAE 312
               SCOP domains d3d4pa1 A:4-148 automated matches                                                                                                                d3d4pa2 A:149-312 automated matches                                                                                                                                  SCOP domains
               CATH domains 3d4pA01 A:4-148 NAD(P)-binding Rossmann-like Domain                                                                                              3d4pA02 A:149-312 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee........--hhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhhhh...ee.......ee.....ee..eehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4p A   4 FKGNKVVLIGNGAVGSSYAFSLVNQSIVDELVIIDLDTEKVRGDVMDLKHATPYSPTTVRVKAGEYSDCHDADLVVICAGAAQKP--TRLDLVSKNLKIFKSIVGEVMASKFDGIFLVATNPVDILAYATWKFSGLPKERVIGSGTILDSARFRLLLSEAFDVAPRSVDAQIIGEHGDTELPVWSHANIAGQPLKTLLEQRPEGKAQIEQIFVQTRDAAYDIIQAKGATYYGVAMGLARITEAIFRNEDAVLTVSALLEGEYEEEDVYIGVPAVINRNGIRNVVEIPLNDEEQSKFAHSAKTLKDIMAE 312
                                    13        23        33        43        53        63        73        83    |  |93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303         
                                                                                                               88 91                                                                                                                                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with LDH1_STAAC | Q5HJD7 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:310
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313
           LDH1_STAAC     4 FKGNKVVLIGNGAVGSSYAFSLVNQSIVDELVIIDLDTEKVRGDVMDLKHATPYSPTTVRVKAGEYSDCHDADLVVICAGAAQKPGETRLDLVSKNLKIFKSIVGEVMASKFDGIFLVATNPVDILAYATWKFSGLPKERVIGSGTILDSARFRLLLSEAFDVAPRSVDAQIIGEHGDTELPVWSHANIAGQPLKTLLEQRPEGKAQIEQIFVQTRDAAYDIIQAKGATYYGVAMGLARITEAIFRNEDAVLTVSALLEGEYEEEDVYIGVPAVINRNGIRNVVEIPLNDEEQSKFAHSAKTLKDIMAEA 313
               SCOP domains d3d4pb1 B:4-148 automated matches                                                                                                                d3d4pb2 B:149-313 automated matches                                                                                                                                   SCOP domains
               CATH domains 3d4pB01 B:4-148 NAD(P)-binding Rossmann-like Domain                                                                                              3d4pB02 B:149-313 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhhhh...ee.......ee.....ee..eehhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d4p B   4 FKGNKVVLIGNGAVGSSYAFSLVNQSIVDELVIIDLDTEKVRGDVMDLKHATPYSPTTVRVKAGEYSDCHDADLVVICAGAAQKPGETRLDLVSKNLKIFKSIVGEVMASKFDGIFLVATNPVDILAYATWKFSGLPKERVIGSGTILDSARFRLLLSEAFDVAPRSVDAQIIGEHGDTELPVWSHANIAGQPLKTLLEQRPEGKAQIEQIFVQTRDAAYDIIQAKGATYYGVAMGLARITEAIFRNEDAVLTVSALLEGEYEEEDVYIGVPAVINRNGIRNVVEIPLNDEEQSKFAHSAKTLKDIMAEA 313
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313

   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  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D4P)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LDH1_STAAC | Q5HJD7)
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:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    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)

UniProtKB/Swiss-Prot
        LDH1_STAAC | Q5HJD73d0o 3h3j

(-) Related Entries Specified in the PDB File

3d0o THE SAME PROTEIN COMPLEXED WITH NAD AND PYRUVATE