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(-) Description

Title :  1.8 A RESOLUTION STRUCTURE OF THE MALATE DEHYDROGENASE FROM PICROPHILUS TORRIDUS IN ITS APO FORM
 
Authors :  R. Talon, D. Madern, E. Girard
Date :  28 Mar 13  (Deposition) - 16 Apr 14  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Keywords :  Hyperacidophile, Oxidoreductase, Tricarboxylic Acid Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Talon, E. Girard, B. Franzetti, D. Madern
Insight Into Structural Evolution Of Extremophilic Proteins
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET20B
    Expression System Vector Type: PLASMID
    Organism Scientific: PICROPHILUS TORRIDUS
    Organism Taxid: 82076
    Other Details: COMPLETE GENE WAS SYNTHESIZED BY GENECUST EUROPE COMPANY

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2PEG11Ligand/IonDI(HYDROXYETHYL)ETHER
3PG61Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
Biological Unit 1 (3, 13)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2PEG11Ligand/IonDI(HYDROXYETHYL)ETHER
3PG61Ligand/Ion1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:13 , GLY A:229 , SER A:230BINDING SITE FOR RESIDUE PEG A1325
02AC2SOFTWAREILE A:24 , HOH A:2334 , HOH A:2335 , HOH A:2336 , ILE B:24BINDING SITE FOR RESIDUE PEG A1326
03AC3SOFTWAREGLU B:41 , GLY B:62 , PHE B:63 , LYS B:70 , HOH B:2054 , HOH B:2072 , HOH B:2073 , HOH B:2323 , ASP C:95 , ILE C:315BINDING SITE FOR RESIDUE CIT B1325
04AC4SOFTWARETYR B:226 , GLY B:229 , SER B:230 , HOH B:2257BINDING SITE FOR RESIDUE PEG B1326
05AC5SOFTWAREPHE A:232 , HOH A:2056 , HOH A:2269 , PHE B:232BINDING SITE FOR RESIDUE PEG B1327
06AC6SOFTWAREGLU B:165 , LEU B:202 , LEU B:203 , PRO B:204 , HOH B:2324 , GLU C:300BINDING SITE FOR RESIDUE PEG B1328
07AC7SOFTWAREASP A:201 , LEU A:203BINDING SITE FOR RESIDUE PEG C1325
08AC8SOFTWAREPRO B:198 , ASP B:201 , HOH B:2215 , HOH B:2233 , ARG C:190 , LYS C:293 , ASN C:295 , HOH C:2223 , HOH C:2305 , HOH C:2330BINDING SITE FOR RESIDUE PG6 C1326
09AC9SOFTWAREALA C:13 , GLY C:229 , SER C:230 , PHE C:232BINDING SITE FOR RESIDUE PEG C1327
10BC1SOFTWAREHOH A:2335 , ILE C:24 , HOH C:2027 , HOH C:2331 , HOH C:2333 , ILE D:24BINDING SITE FOR RESIDUE PEG C1328
11BC2SOFTWARELYS C:43 , PHE C:232 , HOH C:2058 , HOH C:2271 , PHE D:232 , PEG D:1326 , HOH D:2224BINDING SITE FOR RESIDUE PEG D1325
12BC3SOFTWARETYR D:226 , GLY D:229 , SER D:230 , PEG D:1325BINDING SITE FOR RESIDUE PEG D1326
13BC4SOFTWAREALA C:66 , HOH D:2155 , HOH D:2160 , HOH D:2225BINDING SITE FOR RESIDUE PEG D1327

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:126 -Pro A:127
2Asn B:126 -Pro B:127
3Asn C:126 -Pro C:127
4Asn D:126 -Pro D:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BGV)

(-) Exons   (0, 0)

(no "Exon" information available for 4BGV)

(-) 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:323
 aligned with MDH_PICTO | Q6L0C3 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:323
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   
            MDH_PICTO     2 ARSKISVIGAGAVGATVAQTLAIRQTGDIYIFDIVDGLAEGKALDILEGAPHWGYDLDIKGFCTADESKYAEMKGSDVIVVTAGLARKPGMSRDDLLLKNIGIMKSVGEAIKKYSPESKIVVVTNPADIMAYAIYKASGISPERIIGLGGSLDSTRFRTFLAQELNVSFEDVNAFVIGGHGDDMVPFIRYSNVSGIPIEDLLPREKIDEIVKRTRFGGGEIVNLYKTGSAFYAPGISIAVMVESIVNDRKRVIPCAAYITGEHSKTYLVNNLFIGVPIKIGKNGVEKIYDLKFNEDELEAWKKSVESVKKNSAIADDYFAKNQ 324
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.eeeeeeeeee..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhh...eeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bgv A   2 ARSKISVIGAGAVGATVAQTLAIRQTGDIYIFDIVDGLAEGKALDILEGAPHWGYDLDIKGFCTADESKYAEMKGSDVIVVTAGLARKPGMSRDDLLLKNIGIMKSVGEAIKKYSPESKIVVVTNPADIMAYAIYKASGISPERIIGLGGSLDSTRFRTFLAQELNVSFEDVNAFVIGGHGDDMVPFIRYSNVSGIPIEDLLPREKIDEIVKRTRFGGGEIVNLYKTGSAFYAPGISIAVMVESIVNDRKRVIPCAAYITGEHSKTYLVNNLFIGVPIKIGKNGVEKIYDLKFNEDELEAWKKSVESVKKNSAIADDYFAKNQ 324
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   


Chain B from PDB  Type:PROTEIN  Length:323
 aligned with MDH_PICTO | Q6L0C3 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:323
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   
            MDH_PICTO     2 ARSKISVIGAGAVGATVAQTLAIRQTGDIYIFDIVDGLAEGKALDILEGAPHWGYDLDIKGFCTADESKYAEMKGSDVIVVTAGLARKPGMSRDDLLLKNIGIMKSVGEAIKKYSPESKIVVVTNPADIMAYAIYKASGISPERIIGLGGSLDSTRFRTFLAQELNVSFEDVNAFVIGGHGDDMVPFIRYSNVSGIPIEDLLPREKIDEIVKRTRFGGGEIVNLYKTGSAFYAPGISIAVMVESIVNDRKRVIPCAAYITGEHSKTYLVNNLFIGVPIKIGKNGVEKIYDLKFNEDELEAWKKSVESVKKNSAIADDYFAKNQ 324
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.hhh.eee.hhh.ee..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeee..hhhhhhh...eeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bgv B   2 ARSKISVIGAGAVGATVAQTLAIRQTGDIYIFDIVDGLAEGKALDILEGAPHWGYDLDIKGFCTADESKYAEMKGSDVIVVTAGLARKPGMSRDDLLLKNIGIMKSVGEAIKKYSPESKIVVVTNPADIMAYAIYKASGISPERIIGLGGSLDSTRFRTFLAQELNVSFEDVNAFVIGGHGDDMVPFIRYSNVSGIPIEDLLPREKIDEIVKRTRFGGGEIVNLYKTGSAFYAPGISIAVMVESIVNDRKRVIPCAAYITGEHSKTYLVNNLFIGVPIKIGKNGVEKIYDLKFNEDELEAWKKSVESVKKNSAIADDYFAKNQ 324
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   


Chain C from PDB  Type:PROTEIN  Length:323
 aligned with MDH_PICTO | Q6L0C3 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:323
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   
            MDH_PICTO     2 ARSKISVIGAGAVGATVAQTLAIRQTGDIYIFDIVDGLAEGKALDILEGAPHWGYDLDIKGFCTADESKYAEMKGSDVIVVTAGLARKPGMSRDDLLLKNIGIMKSVGEAIKKYSPESKIVVVTNPADIMAYAIYKASGISPERIIGLGGSLDSTRFRTFLAQELNVSFEDVNAFVIGGHGDDMVPFIRYSNVSGIPIEDLLPREKIDEIVKRTRFGGGEIVNLYKTGSAFYAPGISIAVMVESIVNDRKRVIPCAAYITGEHSKTYLVNNLFIGVPIKIGKNGVEKIYDLKFNEDELEAWKKSVESVKKNSAIADDYFAKNQ 324
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.hhh.eee.hhh.ee..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhh...eeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bgv C   2 ARSKISVIGAGAVGATVAQTLAIRQTGDIYIFDIVDGLAEGKALDILEGAPHWGYDLDIKGFCTADESKYAEMKGSDVIVVTAGLARKPGMSRDDLLLKNIGIMKSVGEAIKKYSPESKIVVVTNPADIMAYAIYKASGISPERIIGLGGSLDSTRFRTFLAQELNVSFEDVNAFVIGGHGDDMVPFIRYSNVSGIPIEDLLPREKIDEIVKRTRFGGGEIVNLYKTGSAFYAPGISIAVMVESIVNDRKRVIPCAAYITGEHSKTYLVNNLFIGVPIKIGKNGVEKIYDLKFNEDELEAWKKSVESVKKNSAIADDYFAKNQ 324
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   


Chain D from PDB  Type:PROTEIN  Length:323
 aligned with MDH_PICTO | Q6L0C3 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:323
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   
            MDH_PICTO     2 ARSKISVIGAGAVGATVAQTLAIRQTGDIYIFDIVDGLAEGKALDILEGAPHWGYDLDIKGFCTADESKYAEMKGSDVIVVTAGLARKPGMSRDDLLLKNIGIMKSVGEAIKKYSPESKIVVVTNPADIMAYAIYKASGISPERIIGLGGSLDSTRFRTFLAQELNVSFEDVNAFVIGGHGDDMVPFIRYSNVSGIPIEDLLPREKIDEIVKRTRFGGGEIVNLYKTGSAFYAPGISIAVMVESIVNDRKRVIPCAAYITGEHSKTYLVNNLFIGVPIKIGKNGVEKIYDLKFNEDELEAWKKSVESVKKNSAIADDYFAKNQ 324
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..eee.hhh.eee.hhh.ee..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeee..hhhhhhh...eeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bgv D   2 ARSKISVIGAGAVGATVAQTLAIRQTGDIYIFDIVDGLAEGKALDILEGAPHWGYDLDIKGFCTADESKYAEMKGSDVIVVTAGLARKPGMSRDDLLLKNIGIMKSVGEAIKKYSPESKIVVVTNPADIMAYAIYKASGISPERIIGLGGSLDSTRFRTFLAQELNVSFEDVNAFVIGGHGDDMVPFIRYSNVSGIPIEDLLPREKIDEIVKRTRFGGGEIVNLYKTGSAFYAPGISIAVMVESIVNDRKRVIPCAAYITGEHSKTYLVNNLFIGVPIKIGKNGVEKIYDLKFNEDELEAWKKSVESVKKNSAIADDYFAKNQ 324
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321
   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  (0, 0)

(no "SCOP Domain" information available for 4BGV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MDH_PICTO | Q6L0C3)
molecular function
    GO:0030060    L-malate dehydrogenase activity    Catalysis of the reaction: (S)-malate + NAD+ = oxaloacetate + NADH + H+.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0019752    carboxylic acid metabolic process    The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.

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4bgt 1.70 A RESOLUTION STRUCTURE OF THE MALATE DEHYDROGENASE FROM CHLOROFLEXUS AURANTIACUS
4bgu 1.50 A RESOLUTION STRUCTURE OF THE MALATE DEHYDROGENASE FROM HALOFERAX VOLCANII