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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LACTATE DEHYDROGENASE FROM CRYPTOSPORIDIUM PARVUM COMPLEXED WITH SUBSTRATE (LACTIC ACID) AND COFACTOR (B-NICOTINAMIDE ADENINE DINUCLEOTIDE)
 
Authors :  O. A. Senkovich, D. Chattopadhyay
Date :  10 Jan 06  (Deposition) - 23 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Enzyme_substrate_cofactor Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. A. Senkovich, D. Chattopadhyay
Structure Of Cryptosporidium Parvum Lactate Dehydrogenase I Complex With Substrates And Cofactors
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LACTATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LDH1
    Organism Scientific: CRYPTOSPORIDIUM PARVUM
    Organism Taxid: 5807

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2LAC1Ligand/IonLACTIC ACID
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2LAC1Ligand/IonLACTIC ACID
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2LAC2Ligand/IonLACTIC ACID
3NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (0, 0)

(no "Site" information available for 2FN7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FN7)

(-) 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 2FN7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FN7)

(-) Exons   (0, 0)

(no "Exon" information available for 2FN7)

(-) 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:317
 aligned with Q5CYZ2_CRYPI | Q5CYZ2 from UniProtKB/TrEMBL  Length:337

    Alignment length:317
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       
        Q5CYZ2_CRYPI     17 MIERRKIAVIGSGQIGGNIAYIVGKDNLADVVLFDIAEGIPQGKALDITHSMVMFGSTSKVIGTNDYADISGSDVVIITASIPGRPKDDRSELLFGNARILDSVAEGVKKYCPNAFVICITNPLDVMVSHFQKVSGLPHNKVCGMAGVLDSSRFRTFIAQHFGVNASDVSANVIGGHGDGMVPVTSSVSVGGVPLSSFIKQGLITQEQIDEIVCHTRIAWKEVADNLKTGTAYFAPAAAAVKMAEAYLKDKKAVVPCSAFCSNHYGVKGIYMGVPTIIGKNGVEDILELDLTPLEQKLLGESINEVNTISKVLDNAP  333
               SCOP domains d2fn7a1 A:17-164 Lactate dehydrogenase                                                                                                            d2fn7a2 A:165-333 Lactate dehydrogenase                                                                                                                                     SCOP domains
               CATH domains 2fn7A01 A:17-164 NAD(P)-binding Rossmann-like Domain                                                                                              2fn7A02 A:165-333 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh.......eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeee........eeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fn7 A   17 MIERRKIAVIGSGQIGGNIAYIVGKDNLADVVLFDIAEGIPQGKALDITHSMVMFGSTSKVIGTNDYADISGSDVVIITASIPGRPKDDRSELLFGNARILDSVAEGVKKYCPNAFVICITNPLDVMVSHFQKVSGLPHNKVCGMAGVLDSSRFRTFIAQHFGVNASDVSANVIGGHGDGMVPATSSVSVGGVPLSSFIKQGLITQEQIDEIVCHTRIAWKEVADNLKTGTAYFAPAAAAVKMAEAYLKDKKAVVPCSAFCSNHYGVKGIYMGVPTIIGKNGVEDILELDLTPLEQKLLGESINEVNTISKVLDNAP  333
                                    26      ||37        47|       58        68    ||  77   ||   88        98 ||||||109       119       129  ||   138       148       158       168       178       188       198       208|||||| 214 ||    226       236   ||  244       254       264       274       285       295   ||  306       316       326       
                                           33|          47|                     73A|      81|              100|||||||                    132A|                                                                         209A|||||   216|  223|           240A|  ||                                     283|           299|                                
                                            35           49                      73B       83              103A||||||                     132B                                                                          209B||||    218   225            240B  ||                                      285            301                                
                                                                                                            103B|||||                                                                                                    209C|||                            243A|                                                                                        
                                                                                                             103C||||                                                                                                     209D||                             243B                                                                                        
                                                                                                              105A|||                                                                                                      210A|                                                                                                                         
                                                                                                               105B||                                                                                                       210B                                                                                                                         
                                                                                                                 106|                                                                                                                                                                                                                                    
                                                                                                                  108                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:317
 aligned with Q5CYZ2_CRYPI | Q5CYZ2 from UniProtKB/TrEMBL  Length:337

    Alignment length:317
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       
        Q5CYZ2_CRYPI     17 MIERRKIAVIGSGQIGGNIAYIVGKDNLADVVLFDIAEGIPQGKALDITHSMVMFGSTSKVIGTNDYADISGSDVVIITASIPGRPKDDRSELLFGNARILDSVAEGVKKYCPNAFVICITNPLDVMVSHFQKVSGLPHNKVCGMAGVLDSSRFRTFIAQHFGVNASDVSANVIGGHGDGMVPVTSSVSVGGVPLSSFIKQGLITQEQIDEIVCHTRIAWKEVADNLKTGTAYFAPAAAAVKMAEAYLKDKKAVVPCSAFCSNHYGVKGIYMGVPTIIGKNGVEDILELDLTPLEQKLLGESINEVNTISKVLDNAP  333
               SCOP domains d2fn7b1 B:17-164 Lactate dehydrogenase                                                                                                            d2fn7b2 B:165-333 Lactate dehydrogenase                                                                                                                                     SCOP domains
               CATH domains 2fn7B01 B:17-164 NAD(P)-binding Rossmann-like Domain                                                                                              2fn7B02 B:165-333 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..............hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.....eee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeee........eeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fn7 B   17 MIERRKIAVIGSGQIGGNIAYIVGKDNLADVVLFDIAEGIPQGKALDITHSMVMFGSTSKVIGTNDYADISGSDVVIITASIPGRPKDDRSELLFGNARILDSVAEGVKKYCPNAFVICITNPLDVMVSHFQKVSGLPHNKVCGMAGVLDSSRFRTFIAQHFGVNASDVSANVIGGHGDGMVPATSSVSVGGVPLSSFIKQGLITQEQIDEIVCHTRIAWKEVADNLKTGTAYFAPAAAAVKMAEAYLKDKKAVVPCSAFCSNHYGVKGIYMGVPTIIGKNGVEDILELDLTPLEQKLLGESINEVNTISKVLDNAP  333
                                    26      ||37        47|       58        68    ||  77   ||   88        98 ||||||109       119       129  ||   138       148       158       168       178       188       198       208|||||| 214 ||    226       236   ||  244       254       264       274       285       295   ||  306       316       326       
                                           33|          47|                     73A|      81|              100|||||||                    132A|                                                                         209A|||||   216|  223|           240A|  ||                                     283|           299|                                
                                            35           49                      73B       83              103A||||||                     132B                                                                          209B||||    218   225            240B  ||                                      285            301                                
                                                                                                            103B|||||                                                                                                    209C|||                            243A|                                                                                        
                                                                                                             103C||||                                                                                                     209D||                             243B                                                                                        
                                                                                                              105A|||                                                                                                      210A|                                                                                                                         
                                                                                                               105B||                                                                                                       210B                                                                                                                         
                                                                                                                 106|                                                                                                                                                                                                                                    
                                                                                                                  108
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FN7)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5CYZ2_CRYPI | Q5CYZ2)
molecular function
    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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.

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  1.1.1.27
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 Related Entries

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

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        Q5CYZ2_CRYPI | Q5CYZ2: 4nd1 4nd2 4nd3 4nd4 4nd5

(-) Related Entries Specified in the PDB File

2ewd THE SAME PROTEIN COMPLEXED WITH PYRUVIC ACID AND 3- ACETYLPYRIDINE ADENINE DINUCLEOTIDE
2fm3 THE SAME PROTEIN COMPLEXED WITH PYRUVIC ACID AND B- NICOTINAMIDE ADENINE DINUCLEOTIDE