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(-) Description

Title :  CRYSTAL STRUCTURE OF THE APO FORM OF THERMUS THERMOPHILUS MALATE DEHYDROGENASE
 
Authors :  C. -H. Hsu, C. -H. Hong, Y. -Y. Chang
Date :  25 Apr 13  (Deposition) - 05 Feb 14  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. H. Hung, T. S. Hwang, Y. Y. Chang, H. R. Luo, S. P. Wu, C. H. Hsu
Crystal Structures And Molecular Dynamics Simulations Of Thermophilic Malate Dehydrogenase Reveal Critical Loop Motion For Co-Substrate Binding.
Plos One V. 8 83091 2013
PubMed-ID: 24386145  |  Reference-DOI: 10.1371/JOURNAL.PONE.0083091

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(ED3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET-21
    Fragment: MALATE DEHYDROGENASE
    Gene: MDH
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4KDE)

(-) Sites  (0, 0)

(no "Site" information available for 4KDE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:131 -Pro A:132
2Asn B:131 -Pro B:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KDE)

(-) 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:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4kdea1 A:1-154 Malate dehydrogenase                                                                                                                      d4kdea2 A:155-331 Malate dehydrogenase                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhh.........eeeeee.hhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhh....eeee..........hhhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh....hhh.eee.hhhhhhhhhhhhhhhhh.hhh.ee..eee.......eee....ee..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......eeeeee..hhhhh....eeeeeeeee..eeee......hhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kde A   1 MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQAMKALEGVVMELEDCAFPLLAGLEATDDPKVAFKDADYALLVGAAPRKAGMERRDLLQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSTMFPDLFHAEVDGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGTPEGDWVSMAVPSQGEYGIPEGIVYSFPVTAKDGAYRVVEGLEINEFARKRMEITAQELLDEMEQVKALGLIRKLA 331
                                    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 


Chain B from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4kdeb1 B:1-154 Malate dehydrogenase                                                                                                                      d4kdeb2 B:155-329 Malate dehydrogenase                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhh.........eeeeee.hhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhh....eeee..........hhhhhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh....hhh.eee.hhhhhhhhhhhhhhhhh.hhh.ee..eee.......eee....ee..ee.hhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......eeeeee..hhhhh....eeeeeeeee..eeee......hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kde B   1 MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQAMKALEGVVMELEDCAFPLLAGLEATDDPKVAFKDADYALLVGAAPRKAGMERRDLLQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSTMFPDLFHAEVDGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGTPEGDWVSMAVPSQGEYGIPEGIVYSFPVTAKDGAYRVVEGLEINEFARKRMEITAQELLDEMEQVKALGLIRK 329
                                    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
   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, 4)

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 4KDE)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:131 - Pro A:132   [ RasMol ]  
    Asn B:131 - Pro B:132   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        MDH_THETH | P10584: 1bdm 1bmd 1iz9 1wze 1wzi 1y7t 2cvq 4kdf

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