Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  1.55A RESOLUTION STRUCTURE OF MALATE DEHYDROGENASE FROM SALINIBACTER RUBER
 
Authors :  N. Coquelle, D. Madern
Date :  09 Jun 10  (Deposition) - 13 Oct 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (4x)
Keywords :  Malate Dehydrogenase, Halophile, Molecular Adpatation, Nad, Oxidoreductase, Tricarboxylic Acid Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Coquelle, R. Talon, D. H. Juers, E. Girard, R. Kahn, D. Madern
Gradual Adaptive Changes Of A Protein Facing High Salt Concentrations.
J. Mol. Biol. V. 404 493 2010
PubMed-ID: 20888835  |  Reference-DOI: 10.1016/J.JMB.2010.09.055

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    ChainsX
    EC Number1.1.1.37
    Organism ScientificSALINIBACTER RUBER
    Organism Taxid309807
    StrainDSM 13855

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit X
Biological Unit 1 (4x)X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3NEP)

(-) Sites  (0, 0)

(no "Site" information available for 3NEP)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NEP)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn X:140 -Pro X:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NEP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NEP)

(-) Exons   (0, 0)

(no "Exon" information available for 3NEP)

(-) 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 X from PDB  Type:PROTEIN  Length:305
 aligned with MDH_SALRD | Q2S289 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:312
                                    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  
           MDH_SALRD      1 MKVTVIGAGNVGATVAECVARQDVAKEVVMVDIKDGMPQGKALDMRESSPIHGFDTRVTGTNDYGPTEDSDVCIITAGLPRSPGMSRDDLLAKNTEIVGGVTEQFVEGSPDSTIIVVANPLDVMTYVAYEASGFPTNRVMGMAGVLDTGRFRSFIAEELDVSVRDVQALLMGGHGDTMVPLPRYTTVGGIPVPQLIDDARIEEIVERTKGAGGEIVDLMGTSAWYAPGAAAAEMTEAILKDNKRILPCAAYCDGEYGLDDLFIGVPVKLGAGGVEEVIEVDLDADEKAQLKTSAGHVHSNLDDLQRLRDEGK  312
               SCOP domains d3nepx1 X:22-163 automated matches                                                                                                            d3nepx2 X:164-337 automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains Ldh_1_N-3nepX02 X:22-163                                                                                                                      -Ldh_1_C-3nepX01 X:165-332                                                                                                                                           ----- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhh...eeeee..hhhhh...eeee....-------hhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.eeeeeeeeee..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3nep X   22 MKVTVIGAGNVGATVAECVARQDVAKEVVMVDIKDGMPQGKALDMRESSPIHGFDTRVTGTNDYGPTEDSDVCIITAGL-------RDDLLAKNTEIVGGVTEQFVEGSPDSTIIVVANPLDVMTYVAYEASGFPTNRVMGMAGVLDTGRFRSFIAEELDVSVRDVQALLMGGHGDTMVPLPRYTTVGGIPVPQLIDDARIEEIVERTKGAGGEIVDLMGTSAWYAPGAAAAEMTEAILKDNKRILPCAAYCDGEYGLDDLFIGVPVKLGAGGVEEVIEVDLDADEKAQLKTSAGHVHSNLDDLQRLRDEGK  337
                                    31        41        51        61        71        81        91        |-      |112       122      132A|      141       151       161       171       181       191       201      210B ||    223       233       243       253       263       273      |284       294    || 305       315       325       335  
                                                                                                        100     109                   132A|                                                                          210A| ||                                                             280|              299|                                    
                                                                                                                                       132B                                                                           210B ||                                                              282               301                                    
                                                                                                                                                                                                                         212|                                                                                                                       
                                                                                                                                                                                                                          216                                                                                                                       

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NEP)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: LDH_C (56)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain X   (MDH_SALRD | Q2S289)
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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3nep)
 
  Sites
(no "Sites" information available for 3nep)
 
  Cis Peptide Bonds
    Asn X:140 - Pro X:141   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3nep
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MDH_SALRD | Q2S289
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.1.1.37
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  MDH_SALRD | Q2S289
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3NEP)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3NEP)