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(-) Description

Title :  STRUCTURE OF MALATE DEHYDROGENASE FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  N. K. Lokanath, N. Kunishima, Riken Structural Genomics/Proteomic Initiative (Rsgi)
Date :  26 Jan 04  (Deposition) - 29 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dehydrogenase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. K. Lokanath, N. Kunishima
Structure Of Malate Dehydrogenase From Pyrococcus Horikoshi Ot3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE11Mod. Amino AcidSELENOMETHIONINE
3NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (3, 26)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE22Mod. Amino AcidSELENOMETHIONINE
3NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:4 , ARG A:50 , VAL A:52 , HIS A:55 , HIS A:127 , GLY A:129 , ILE A:130 , ALA A:131 , SER A:151 , THR A:167 , PRO A:169 , LEU A:182 , LEU A:183 , ASP A:184 , MSE A:185 , ALA A:186 , PRO A:191 , GLU A:238 , HIS A:243 , LYS A:244 , TYR A:246 , TRP A:320 , HIS A:322 , GLY A:323 , GLU A:324 , LYS A:325 , GLY A:326 , HOH A:410 , HOH A:412 , HOH A:413 , HOH A:433 , HOH A:447 , HOH A:458 , HOH A:511 , HOH A:512 , HOH A:513BINDING SITE FOR RESIDUE NDP A 401
2AC2SOFTWAREALA A:156 , PRO A:157 , THR A:158 , GLY A:159 , GLY A:160 , LEU A:231 , PRO A:232 , PHE A:236 , HIS A:313 , PHE A:316 , HOH A:480BINDING SITE FOR RESIDUE GOL A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V9N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V9N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V9N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V9N)

(-) Exons   (0, 0)

(no "Exon" information available for 1V9N)

(-) 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:348
 aligned with MDH_PYRHO | O59028 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:360
                                    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       320       330       340       350       360
            MDH_PYRHO     1 MFEKGYVDENYIRVPKDRLFSFIVRVLTKLGVPEEDAKIVADNLVMADLRGVESHGVQRLKRYVDGIISGGVNLHPKIRVIREGPSYALIDGDEGLGQVVGYRSMKLAIKKAKDTGIGIVIARNSNHYGIAGYYALMAAEEGMIGISMTNSRPLVAPTGGIERILGTNPIALAAPTKDKPFLLDMATSVVPIGKLEVYRRKGKDIPEGWAINREGNITTKVEEVFNGGALLPLGGFGELLGGHKGYGLSLMVDILSGILSGGTWSKYVKNTSEKGSNVCHFFMVIDIEHFIPLEEFKEKISQMIEEIKSSRKHPEFERIWIHGEKGFLTMETRLKLGIPIYRKVLEELNEIAKRVGVEGL 360
               SCOP domains d1v9na_ A: automated matches                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------Ldh_2-1v9nA01 A:12-351                                                                                                                                                                                                                                                                                                                              --------- Pfam domains
         Sec.struct. author ..........eeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.........eeeeee..eeeee....hhhhhhhhhhhhhhhhhhhhheeeeeeeee.....hhhhhhhhhh...eeeeee....................eeeee......eeeee...........------------................................hhhhhhhhhhhhhhhhh......hhhhh.........eeeeeeee.hhhh.hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhheeeehhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v9n A   1 mFEKGYVDENYIRVPKDRLFSFIVRVLTKLGVPEEDAKIVADNLVmADLRGVESHGVQRLKRYVDGIISGGVNLHPKIRVIREGPSYALIDGDEGLGQVVGYRSmKLAIKKAKDTGIGIVIARNSNHYGIAGYYALmAAEEGmIGISmTNSRPLVAPTGGIERILGTNPIALAAPTKDKPFLLDmATSVVPIGKLE------------WAINREGNITTKVEEVFNGGALLPLGGFGELLGGHKGYGLSLmVDILSGILSGGTWSKYVKNTSEKGSNVCHFFmVIDIEHFIPLEEFKEKISQmIEEIKSSRKHPEFERIWIHGEKGFLTmETRLKLGIPIYRKVLEELNEIAKRVGVEGL 360
                            |       10        20        30        40     |  50        60        70        80        90       100    |  110       120       130      |140  |    150       160       170       180    |  190     |   -       210       220       230       240       250|      260       270       280  |    290       300  |    310       320       330       340       350       360
                            |                                           46-MSE                                                    105-MSE                         137-MSE |    |                                  185-MSE    196          209                                       251-MSE                         283-MSE             303-MSE                    330-MSE                          
                            1-MSE                                                                                                                                       143-MSE|                                                                                                                                                                                                                    
                                                                                                                                                                             148-MSE
   Legend:   → Mismatch (orange background)
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  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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1V9N)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Ldh_2] (7)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (MDH_PYRHO | O59028)
molecular function
    GO:0030060    L-malate dehydrogenase activity    Catalysis of the reaction: (S)-malate + NAD+ = oxaloacetate + NADH + H+.
    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.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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.
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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