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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  SINGLE POINT MUTANT OF THERMUS THERMOPHILUS LACTATE DEHYDROGENASE
 
Authors :  E. De Mendoza-Barbera, F. M. D. Vellieux
Date :  10 Nov 11  (Deposition) - 28 Dec 11  (Release) - 30 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase, Thermophile (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Colletier, A. Aleksandrov, N. Coquelle, S. Mraihi, E. De Mendoza-Barbera, M. Field, D. Madern
Sampling The Conformational Energy Landscape Of A Hyperthermophilic Protein By Engineering Key Substitutions
Mol. Biol. Evol. V. 29 1683 2012
PubMed-ID: 22319152  |  Reference-DOI: 10.1093/MOLBEV/MSS015

(-) 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: PTTHLDH12
    Expression System Strain: DH5[ALPHA]
    Expression System Taxid: 668369
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    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 4A73)

(-) Sites  (0, 0)

(no "Site" information available for 4A73)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A73)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Asn A:140 -Pro A:141
2Asn B:140 -Pro B:141
3Thr C:108 -Arg C:109
4Arg C:109 -Leu C:110
5Asn C:140 -Pro C:141
6Pro D:105 -Gly D:106
7Asn D:140 -Pro D:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A73)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1L_LDHPS00064 L-lactate dehydrogenase active site.LDH_THET8169-175
 
 
 		  4A:192-198
B:192-198
C:192-198
D:192-198

(-) Exons   (0, 0)

(no "Exon" information available for 4A73)

(-) 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:310
 aligned with LDH_THET8 | Q5SJA1 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:310
                                    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       300       310
           LDH_THET8      1 MKVGIVGSGMVGSATAYALALLGVAREVVLVDLDRKLAQAHAEDILHATPFAHPVWVRAGSYGDLEGARAVVLAAGVAQRPGETRLQLLDRNAQVFAQVVPRVLEAAPEAVLLVATNPVDVMTQVAYRLSGLPPGRVVGSGTILDTARFRALLAEYLRVAPQSVHAYVLGEHGDSEVLVWSSAQVGGVPLLEFAEARGRALSPEDRARIDEGVRRAAYRIIEGKGATYYGIGAGLARLVRAILTDEKGVYTVSAFTPEVEGVLEVSLSLPRILGAGGVEGTVYPSLSPEEREALRRSAEILKEAAFALGF  310
               SCOP domains d4a73a1 A:22-164 automated matches                                                                                                           d4a73a2 A:165-331 automated matches                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh...eeeeehhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhhhh.hhh.eeeeee.......eeeeeeeee..eehhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeeeeeeeeeee..eeeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4a73 A   22 MKVGIVGSGMVGSATAYALALLGVAREVVLVDLDRKLAQAHAEDILHATPFAHPVWVRAGSYGDLEGARAVVLAAGVAQRPGETRLQLLDRNAQVFAQVVPRVLEAAPEAVLLVATNPVDVMTQVAYRLSGLPPGRVVGSGTILDTARFRALLAEYLRVAPQSVHAYVLGEHGDSEVLVWSSAQVGGVPLLEFAEARGAALSPEDRARIDEGVRRAAYRIIEGKGATYYGIGAGLARLVRAILTDEKGVYTVSAFTPEVEGVLEVSLSLPRILGAGGVEGTVYPSLSPEEREALRRSAEILKEAAFALGF  331
                                    31        41        51        61        71        83        93       103|      114       124       133       143       153       163       173       183       193       203     |210A|      219       229       239       249       259       269       279   ||  290       301       311       321       331
                                                                                     80|                 103|                       132A|                                                                         209A|||||                                                                      283|           299|                              
                                                                                      83                  105                        132B                                                                          209B||||                                                                       285            301                              
                                                                                                                                                                                                                    209C|||                                                                                                                       
                                                                                                                                                                                                                     209D||                                                                                                                       
                                                                                                                                                                                                                      210A|                                                                                                                       
                                                                                                                                                                                                                       210B                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:309
 aligned with LDH_THET8 | Q5SJA1 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:310
                                    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       300       310
           LDH_THET8      1 MKVGIVGSGMVGSATAYALALLGVAREVVLVDLDRKLAQAHAEDILHATPFAHPVWVRAGSYGDLEGARAVVLAAGVAQRPGETRLQLLDRNAQVFAQVVPRVLEAAPEAVLLVATNPVDVMTQVAYRLSGLPPGRVVGSGTILDTARFRALLAEYLRVAPQSVHAYVLGEHGDSEVLVWSSAQVGGVPLLEFAEARGRALSPEDRARIDEGVRRAAYRIIEGKGATYYGIGAGLARLVRAILTDEKGVYTVSAFTPEVEGVLEVSLSLPRILGAGGVEGTVYPSLSPEEREALRRSAEILKEAAFALGF  310
               SCOP domains d4a73b1 B:22-164 automated matches                                                                                                           d4a73b2 B:165-331 automated matches                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh...eeee.hhhhhh.eeeeee...........h-hhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhhh...hhh.ee..ee.......ee.....ee...hhhhhhh......hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..eeeeeeeeeeee..eeeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4a73 B   22 MKVGIVGSGMVGSATAYALALLGVAREVVLVDLDRKLAQAHAEDILHATPFAHPVWVRAGSYGDLEGARAVVLAAGVAQRPGETR-QLLDRNAQVFAQVVPRVLEAAPEAVLLVATNPVDVMTQVAYRLSGLPPGRVVGSGTILDTARFRALLAEYLRVAPQSVHAYVLGEHGDSEVLVWSSAQVGGVPLLEFAEARGAALSPEDRARIDEGVRRAAYRIIEGKGATYYGIGAGLARLVRAILTDEKGVYTVSAFTPEVEGVLEVSLSLPRILGAGGVEGTVYPSLSPEEREALRRSAEILKEAAFALGF  331
                                    31        41        51        61        71        83        93       103|   | |114       124       133       143       153       163       173       183       193       203     |210A|      219       229       239       249       259       269       279   ||  290       301       311       321       331
                                                                                     80|                 103| 109 |                 132A|                                                                         209A|||||                                                                      283|           299|                              
                                                                                      83                  105   111                  132B                                                                          209B||||                                                                       285            301                              
                                                                                                                                                                                                                    209C|||                                                                                                                       
                                                                                                                                                                                                                     209D||                                                                                                                       
                                                                                                                                                                                                                      210A|                                                                                                                       
                                                                                                                                                                                                                       210B                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:309
 aligned with LDH_THET8 | Q5SJA1 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:310
                                    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       300       310
           LDH_THET8      1 MKVGIVGSGMVGSATAYALALLGVAREVVLVDLDRKLAQAHAEDILHATPFAHPVWVRAGSYGDLEGARAVVLAAGVAQRPGETRLQLLDRNAQVFAQVVPRVLEAAPEAVLLVATNPVDVMTQVAYRLSGLPPGRVVGSGTILDTARFRALLAEYLRVAPQSVHAYVLGEHGDSEVLVWSSAQVGGVPLLEFAEARGRALSPEDRARIDEGVRRAAYRIIEGKGATYYGIGAGLARLVRAILTDEKGVYTVSAFTPEVEGVLEVSLSLPRILGAGGVEGTVYPSLSPEEREALRRSAEILKEAAFALGF  310
               SCOP domains d4a73c1 C:22-164 automated matches                                                                                                           d4a73c2 C:165-331 automated matches                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh...eeee.hhhhhh...eeee.............-hhhhhh.hhhhhhhhhhh.....eeee...hhhhhhhhhhhhhh.....eee..hhhhhhhhhhhhhhhhh.hhh.ee..................ee...hhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeeeeeeee..eeeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4a73 C   22 MKVGIVGSGMVGSATAYALALLGVAREVVLVDLDRKLAQAHAEDILHATPFAHPVWVRAGSYGDLEGARAVVLAAGVAQRPGETRL-LLDRNAQVFAQVVPRVLEAAPEAVLLVATNPVDVMTQVAYRLSGLPPGRVVGSGTILDTARFRALLAEYLRVAPQSVHAYVLGEHGDSEVLVWSSAQVGGVPLLEFAEARGAALSPEDRARIDEGVRRAAYRIIEGKGATYYGIGAGLARLVRAILTDEKGVYTVSAFTPEVEGVLEVSLSLPRILGAGGVEGTVYPSLSPEEREALRRSAEILKEAAFALGF  331
                                    31        41        51        61        71        83        93       103|    | 114       124       133       143       153       163       173       183       193       203     |210A|      219       229       239       249       259       269       279   ||  290       301       311       321       331
                                                                                     80|                 103|  110 |                132A|                                                                         209A|||||                                                                      283|           299|                              
                                                                                      83                  105    112                 132B                                                                          209B||||                                                                       285            301                              
                                                                                                                                                                                                                    209C|||                                                                                                                       
                                                                                                                                                                                                                     209D||                                                                                                                       
                                                                                                                                                                                                                      210A|                                                                                                                       
                                                                                                                                                                                                                       210B                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:310
 aligned with LDH_THET8 | Q5SJA1 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:310
                                    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       300       310
           LDH_THET8      1 MKVGIVGSGMVGSATAYALALLGVAREVVLVDLDRKLAQAHAEDILHATPFAHPVWVRAGSYGDLEGARAVVLAAGVAQRPGETRLQLLDRNAQVFAQVVPRVLEAAPEAVLLVATNPVDVMTQVAYRLSGLPPGRVVGSGTILDTARFRALLAEYLRVAPQSVHAYVLGEHGDSEVLVWSSAQVGGVPLLEFAEARGRALSPEDRARIDEGVRRAAYRIIEGKGATYYGIGAGLARLVRAILTDEKGVYTVSAFTPEVEGVLEVSLSLPRILGAGGVEGTVYPSLSPEEREALRRSAEILKEAAFALGF  310
               SCOP domains d4a73d1 D:22-164 automated matches                                                                                                           d4a73d2 D:165-331 automated matches                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhh...eeeeehhhhhh...eeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.....eee..hhhhhhhhhhhhhhhh..hhhhh...ee.......ee.....ee..eehhhhhhhh...........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeeeeeeee..eeeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------L_LDH  --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4a73 D   22 MKVGIVGSGMVGSATAYALALLGVAREVVLVDLDRKLAQAHAEDILHATPFAHPVWVRAGSYGDLEGARAVVLAAGVAQRPGETRLQLLDRNAQVFAQVVPRVLEAAPEAVLLVATNPVDVMTQVAYRLSGLPPGRVVGSGTILDTARFRALLAEYLRVAPQSVHAYVLGEHGDSEVLVWSSAQVGGVPLLEFAEARGAALSPEDRARIDEGVRRAAYRIIEGKGATYYGIGAGLARLVRAILTDEKGVYTVSAFTPEVEGVLEVSLSLPRILGAGGVEGTVYPSLSPEEREALRRSAEILKEAAFALGF  331
                                    31        41        51        61        71        83        93       103|      114       124       133       143       153       163       173       183       193       203     |210A|      219       229       239       249       259       269       279   ||  290       301       311       321       331
                                                                                     80|                 103|                       132A|                                                                         209A|||||                                                                      283|           299|                              
                                                                                      83                  105                        132B                                                                          209B||||                                                                       285            301                              
                                                                                                                                                                                                                    209C|||                                                                                                                       
                                                                                                                                                                                                                     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  (0, 0)

(no "CATH Domain" information available for 4A73)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A73)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (LDH_THET8 | Q5SJA1)
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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  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4a73)
 
  Sites
(no "Sites" information available for 4a73)
 
  Cis Peptide Bonds
    Arg C:109 - Leu C:110   [ RasMol ]  
    Asn A:140 - Pro A:141   [ RasMol ]  
    Asn B:140 - Pro B:141   [ RasMol ]  
    Asn C:140 - Pro C:141   [ RasMol ]  
    Asn D:140 - Pro D:141   [ RasMol ]  
    Pro D:105 - Gly D:106   [ RasMol ]  
    Thr C:108 - Arg C:109   [ RasMol ]  
 

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 Databases and Analysis Tools

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  4a73
    Family and Domain Information: ProDom | SYSTERS
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  LDH_THET8 | Q5SJA1
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  1.1.1.27
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 Related Entries

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

UniProtKB/Swiss-Prot
        LDH_THET8 | Q5SJA1: 2e37 2v6m 2v7p 2xxb 2xxj 3zzn

(-) Related Entries Specified in the PDB File

2v6m CRYSTAL STRUCTURE OF LACTATE DEHYDROGENASE FROM THERMUS THERMOPHILUS HB8 (APO FORM)
2v7p CRYSTAL STRUCTURE OF LACTATE DEHYDROGENASE FROM THERMUS THERMOPHILUS HB8 (HOLO FORM)
2xxb PENTA-MUTANT OF THERMUS THERMOPHILUS LACTATE DEHYDROGENASE, COMPLEX WITH AMP
2xxj PENTA MUTANT OF LACTATE DEHYDROGENASE FROM THERMUS THERMOPHILUS, TERNARY COMPLEX
3zzn 5-MUTANT (R79W, R151A, E279A, E299A,E313A) LACTATE- DEHYDROGENASE FROM THERMUS THERMOPHILLUS