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(-) Description

Title :  CRYSTAL STRUCTURE OF LACTATE DEHYDROGENASE FROM DEINOCOCCUS RADIODURANS (APO FORM)
 
Authors :  N. Coquelle, E. Fioravanti, M. Weik, F. Vellieux
Date :  16 Jul 07  (Deposition) - 25 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase, Radioresistance, Lactate Dehydrogenase, Ldh, Nad, Cytoplasm, Mesophilic, Glycolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Coquelle, E. Fioravanti, M. Weik, F. Vellieux, D. Madern
Activity, Stability And Structural Studies Of Lactate Dehydrogenases Adapted To Extreme Thermal Environments.
J. Mol. Biol. V. 374 547 2007
PubMed-ID: 17936781  |  Reference-DOI: 10.1016/J.JMB.2007.09.049

(-) Compounds

Molecule 1 - L-LACTATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKDL302
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 562
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Synonym: L-LDH

 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 2V6B)

(-) Sites  (0, 0)

(no "Site" information available for 2V6B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V6B)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Asn A:140 -Pro A:141
2Asn B:140 -Pro B:141
3Asp C:132B-Pro C:132A
4Asn C:140 -Pro C:141
5Asn D:140 -Pro D:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V6B)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LDHPS00064 L-lactate dehydrogenase active site.LDH_DEIRA167-173
 
 
 		  4A:192-198
B:192-198
C:192-198
D:192-198

(-) Exons   (0, 0)

(no "Exon" information available for 2V6B)

(-) 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:274
 aligned with LDH_DEIRA | P50933 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:297
                                    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       
           LDH_DEIRA      1 MKVGVVGTGFVGSTAAFALVLRGSCSELVLVDRDEDRAQAEAEDIAHAAPVSHGTRVWHGGHSELADAQVVILTAGANQKPGESRLDLLEKNADIFRELVPQITRAAPDAVLLVTSNPVDLLTDLATQLAPGQPVIGSGTVLDSARFRHLMAQHAGVDGTHAHGYVLGEHGDSEVLAWSSAMVAGMPVADFMQAQNLPWNEQVRAKIDEGTRNAAASIIEGKRATYYGIGAALARITEAVLRDRRAVLTVSAPTPEYGVSLSLPRVVGRQGVLSTLHPKLTGDEQQKLEQSAGVLRG  297
               SCOP domains d2v6ba1 A:22-164 automated matches                                                                                                         d2v6ba2 A:165-324 automated matches                                                                                                                            SCOP domains
               CATH domains 2v6bA01 A:22-164 NAD(P)-binding Rossmann-like Domain                                                                                       2v6bA02 A:165-324 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain            2                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhh.........eeeeehhhhhh...eeee..------------hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eee..hhhhhhhhhhhhhhhhh.hhh.ee..eee.....eee.hhh.ee..eehhhhhhhhh...hhhhhhhhhhhhh.-----------.hhhhhhhhhhhhhhhhh...eeeeeeee......eeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2v6b A   22 MKVGVVGTGFVGSTAAFALVLRGSCSELVLVDRDEDRAQAEAEDIAHAAPVSHGTRVWHGGHSELADAQVVILTA------------LLEKNADIFRELVPQITRAAPDAVLLVTSNPVDLLTDLATQLAPGQPVIGSGTVLDSARFRHLMAQHAGVDGTHAHGYVLGEHGDSEVLAWSSAMVAGMPVADFMQAQNLPWNEQVRAKIDEGTRN-----------TYYGIGAALARITEAVLRDRRAVLTVSAPTPEYGVSLSLPRVVGRQGVLSTLHPKLTGDEQQKLEQSAGVLRG  324
                                    31        41        51        61        71        83        93    |    -       114       124       133       143       153  ||   165       175       185       195       205   ||||211       221       231  |      -    |  251       261       271      |286       296  ||   307       317       
                                                                                     80|             98          112                132A|                     156|                                              209A|||||                     234         246                             278||           299|                       
                                                                                      83                                             132B                      159                                               209B||||                                                                  283|            301                       
                                                                                                                                                                                                                  209C|||                                                                   285                                      
                                                                                                                                                                                                                   209D||                                                                                                            
                                                                                                                                                                                                                    210A|                                                                                                            
                                                                                                                                                                                                                     210B                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:282
 aligned with LDH_DEIRA | P50933 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:299
                                    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         
           LDH_DEIRA      1 MKVGVVGTGFVGSTAAFALVLRGSCSELVLVDRDEDRAQAEAEDIAHAAPVSHGTRVWHGGHSELADAQVVILTAGANQKPGESRLDLLEKNADIFRELVPQITRAAPDAVLLVTSNPVDLLTDLATQLAPGQPVIGSGTVLDSARFRHLMAQHAGVDGTHAHGYVLGEHGDSEVLAWSSAMVAGMPVADFMQAQNLPWNEQVRAKIDEGTRNAAASIIEGKRATYYGIGAALARITEAVLRDRRAVLTVSAPTPEYGVSLSLPRVVGRQGVLSTLHPKLTGDEQQKLEQSAGVLRGFK  299
               SCOP domains d2v6bb1 B:22-164 automated matches                                                                                                         d2v6bb2 B:165-326 automated matches                                                                                                                              SCOP domains
               CATH domains 2v6bB01 B:22-164 NAD(P)-binding Rossmann-like Domain                                                                                       2v6bB02 B:165-326 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain             2                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhh..hhhhh.eeee.hhhhhh...eeee....-----.hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhhh....hhhhhhhhhhhhh------------.hhhhhhhhhhhhhhhhh...eee..eee......eee..eeee..eeeee.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2v6b B   22 MKVGVVGTGFVGSTAAFALVLRGSCSELVLVDRDEDRAQAEAEDIAHAAPVSHGTRVWHGGHSELADAQVVILTAGA-----ESRLDLLEKNADIFRELVPQITRAAPDAVLLVTSNPVDLLTDLATQLAPGQPVIGSGTVLDSARFRHLMAQHAGVDGTHAHGYVLGEHGDSEVLAWSSAMVAGMPVADFMQAQNLPWNEQVRAKIDEGTR------------TYYGIGAALARITEAVLRDRRAVLTVSAPTPEYGVSLSLPRVVGRQGVLSTLHPKLTGDEQQKLEQSAGVLRGFK  326
                                    31        41        51        61        71        83        93      |  -  |    114       124       133       143       153  ||   165       175       185       195       205   ||||211       221       231 |       -    |  251       261       271      |286       296  ||   307       317         
                                                                                     80|              100   107                     132A|                     156|                                              209A|||||                    233          246                             278||           299|                         
                                                                                      83                                             132B                      159                                               209B||||                                                                  283|            301                         
                                                                                                                                                                                                                  209C|||                                                                   285                                        
                                                                                                                                                                                                                   209D||                                                                                                              
                                                                                                                                                                                                                    210A|                                                                                                              
                                                                                                                                                                                                                     210B                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:281
 aligned with LDH_DEIRA | P50933 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:299
                                    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         
           LDH_DEIRA      1 MKVGVVGTGFVGSTAAFALVLRGSCSELVLVDRDEDRAQAEAEDIAHAAPVSHGTRVWHGGHSELADAQVVILTAGANQKPGESRLDLLEKNADIFRELVPQITRAAPDAVLLVTSNPVDLLTDLATQLAPGQPVIGSGTVLDSARFRHLMAQHAGVDGTHAHGYVLGEHGDSEVLAWSSAMVAGMPVADFMQAQNLPWNEQVRAKIDEGTRNAAASIIEGKRATYYGIGAALARITEAVLRDRRAVLTVSAPTPEYGVSLSLPRVVGRQGVLSTLHPKLTGDEQQKLEQSAGVLRGFK  299
               SCOP domains d2v6bc1 C:22-164 automated matches                                                                                                         d2v6bc2 C:165-326 automated matches                                                                                                                              SCOP domains
               CATH domains 2v6bC01 C:22-164 NAD(P)-binding Rossmann-like Domain                                                                                       2v6bC02 C:165-326 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain            2                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhh......eeeeehhhhhh...eeee...-------hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhhhh...hhhhhhhhhhhhh.-----------.hhhhhhhhhhhhhhhhh...eeeeeeee......eeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2v6b C   22 MKVGVVGTGFVGSTAAFALVLRGSCSELVLVDRDEDRAQAEAEDIAHAAPVSHGTRVWHGGHSELADAQVVILTAG-------SRLDLLEKNADIFRELVPQITRAAPDAVLLVTSNPVDLLTDLATQLAPGQPVIGSGTVLDSARFRHLMAQHAGVDGTHAHGYVLGEHGDSEVLAWSSAMVAGMPVADFMQAQNLPWNEQVRAKIDEGTRN-----------TYYGIGAALARITEAVLRDRRAVLTVSAPTPEYGVSLSLPRVVGRQGVLSTLHPKLTGDEQQKLEQSAGVLRGFK  326
                                    31        41        51        61        71        83        93     |   -   |   114       124       133       143       153  ||   165       175       185       195       205   ||||211       221       231  |      -    |  251       261       271      |286       296  ||   307       317         
                                                                                     80|              99     108                    132A|                     156|                                              209A|||||                     234         246                             278||           299|                         
                                                                                      83                                             132B                      159                                               209B||||                                                                  283|            301                         
                                                                                                                                                                                                                  209C|||                                                                   285                                        
                                                                                                                                                                                                                   209D||                                                                                                              
                                                                                                                                                                                                                    210A|                                                                                                              
                                                                                                                                                                                                                     210B                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:279
 aligned with LDH_DEIRA | P50933 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:298
                                    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        
           LDH_DEIRA      1 MKVGVVGTGFVGSTAAFALVLRGSCSELVLVDRDEDRAQAEAEDIAHAAPVSHGTRVWHGGHSELADAQVVILTAGANQKPGESRLDLLEKNADIFRELVPQITRAAPDAVLLVTSNPVDLLTDLATQLAPGQPVIGSGTVLDSARFRHLMAQHAGVDGTHAHGYVLGEHGDSEVLAWSSAMVAGMPVADFMQAQNLPWNEQVRAKIDEGTRNAAASIIEGKRATYYGIGAALARITEAVLRDRRAVLTVSAPTPEYGVSLSLPRVVGRQGVLSTLHPKLTGDEQQKLEQSAGVLRGF  298
               SCOP domains d2v6bd1 D:22-164 automated matches                                                                                                         d2v6bd2 D:165-325 automated matches                                                                                                                             SCOP domains
               CATH domains 2v6bD01 D:22-164 NAD(P)-binding Rossmann-like Domain                                                                                       2v6bD02 D:165-325 L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain             2                                                                         CATH domains
           Pfam domains (1) Ldh_1_N-2v6bD05 D:22-163                                                                                                                  -Ldh_1_C-2v6bD01 D:165-325                                                                                                                                       Pfam domains (1)
           Pfam domains (2) Ldh_1_N-2v6bD06 D:22-163                                                                                                                  -Ldh_1_C-2v6bD02 D:165-325                                                                                                                                       Pfam domains (2)
           Pfam domains (3) Ldh_1_N-2v6bD07 D:22-163                                                                                                                  -Ldh_1_C-2v6bD03 D:165-325                                                                                                                                       Pfam domains (3)
           Pfam domains (4) Ldh_1_N-2v6bD08 D:22-163                                                                                                                  -Ldh_1_C-2v6bD04 D:165-325                                                                                                                                       Pfam domains (4)
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhh........eeeeehhhhhh...eeee....-------hhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eee..hhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhhh....hhhhhhhhhhhhh------------.hhhhhhhhhhhhhhhhhh..eee..eee......eee..eeee..eeeee.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2v6b D   22 MKVGVVGTGFVGSTAAFALVLRGSCSELVLVDRDEDRAQAEAEDIAHAAPVSHGTRVWHGGHSELADAQVVILTAGA-------RLDLLEKNADIFRELVPQITRAAPDAVLLVTSNPVDLLTDLATQLAPGQPVIGSGTVLDSARFRHLMAQHAGVDGTHAHGYVLGEHGDSEVLAWSSAMVAGMPVADFMQAQNLPWNEQVRAKIDEGTR------------TYYGIGAALARITEAVLRDRRAVLTVSAPTPEYGVSLSLPRVVGRQGVLSTLHPKLTGDEQQKLEQSAGVLRGF  325
                                    31        41        51        61        71        83        93      |  -    |  114       124       133       143       153  ||   165       175       185       195       205   ||||211       221       231 |       -    |  251       261       271      |286       296  ||   307       317        
                                                                                     80|              100     109                   132A|                     156|                                              209A|||||                    233          246                             278||           299|                        
                                                                                      83                                             132B                      159                                               209B||||                                                                  283|            301                        
                                                                                                                                                                                                                  209C|||                                                                   285                                       
                                                                                                                                                                                                                   209D||                                                                                                             
                                                                                                                                                                                                                    210A|                                                                                                             
                                                                                                                                                                                                                     210B
   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, 8)

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

(-) Pfam Domains  (2, 8)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (LDH_DEIRA | P50933)
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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    Asn A:140 - Pro A:141   [ RasMol ]  
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  2v6b
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  LDH_DEIRA | P50933
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 Related Entries

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