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(-) Description

Title :  STRUCTURE OF SUBSTRATE/COFACTOR-FREE D-AMINO ACID DEHYDROGENASE
 
Authors :  H. Sakuraba, T. Seto, J. Hayashi, H. Akita, K. Yoneda, T. Ohshima
Date :  26 Sep 16  (Deposition) - 12 Apr 17  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Hayashi, T. Seto, H. Akita, M. Watanabe, T. Hoshino, K. Yoneda, T. Ohshima, H. Sakuraba
Structure-Based Engineering Of An Artificially Generated Nadp(+)-Dependent D-Amino Acid Dehydrogenase
Appl. Environ. Microbiol. V. 83 2017
PubMed-ID: 28363957  |  Reference-DOI: 10.1128/AEM.00491-17

(-) Compounds

Molecule 1 - MESO-DIAMINOPIMELATE D-DEHYDROGENASE
    Chains: A, B
    EC Number: 1.4.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: ROSSETA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DDH
    Mutation: YES
    Organism Scientific: UREIBACILLUS THERMOSPHAERICUS
    Organism Taxid: 51173
    Synonym: MESO-DAP DEHYDROGENASE

 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 5GZ1)

(-) Sites  (0, 0)

(no "Site" information available for 5GZ1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GZ1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asp A:124 -Pro A:125
2Gly A:149 -Lys A:150
3Asp B:124 -Pro B:125
4Gly B:149 -Lys B:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GZ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GZ1)

(-) Exons   (0, 0)

(no "Exon" information available for 5GZ1)

(-) 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:320
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhh...eeeeeeee..hhhhh.......eee.hhhhhhh....eeee.....hhhhhhhhhhh...eee....hhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhh..eeeeeee..eee.........eeeeeeeeeehhhhhhhhhh......hhhhheeeeeeeee....hhhhhhhhhhh.......eeeee.hhhhhhhhh....eeeeeeeeee.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gz1 A   2 SKIRIGIVGYGNLGRGVEAAIQQNPDMELVAVFTRRDPKTVAVKSNVKVLHVDDAQSYKDEIDVMILCGGSATDLPEQGPYFAQYFNTIDSFDTHARIPDYFDAVNAAAEQSGKVAIISVGWDPGLFSLNRLLGEVVLPVGNTYTFWGKGVSLGAIRRIQGVKNAVQYIIPIDEAVNRVRSGENPELSTREKHAMECFVVLEEGADPAKVEHEIKTMPFDEYDTTVHFISEEELKQNHSGMPNGGFVIRSGKSDEGHKQIIEFSLNLESNPMFTSSALVAYARAAYRLSQNGDKGAKTVFDIPFGLLSPKSPEDLRKELL 326
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  ||   164       174       184       194       204       214       226       236       246       256       266       276       286       296       306       316       326
                                                                                                                                                                                  154|                                                             222|                                                                                                     
                                                                                                                                                                                   158                                                              225                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:325
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhh...eeeeeeee..hhhhh......eeee.hhhhhhhhhh.eeee.....hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhh..eeeeeee..eehhhhhhhhhh...eeeeeeeeeehhhhhhhhhh......hhhhheeeeeeeee....hhhhhhhhhhh.........eeeee.hhhhhhhhh....eeeeeeeeee.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gz1 B   2 SKIRIGIVGYGNLGRGVEAAIQQNPDMELVAVFTRRDPKTVAVKSNVKVLHVDDAQSYKDEIDVMILCGGSATDLPEQGPYFAQYFNTIDSFDTHARIPDYFDAVNAAAEQSGKVAIISVGWDPGLFSLNRLLGEVVLPVGNTYTFWGKGVSLGHSGAIRRIQGVKNAVQYIIPIDEAVNRVRSGENPELSTREKHAMECFVVLEEGADPAKVEHEIKTMPNYFDEYDTTVHFISEEELKQNHSGMPNGGFVIRSGKSDEGHKQIIEFSLNLESNPMFTSSALVAYARAAYRLSQNGDKGAKTVFDIPFGLLSPKSPEDLRKELL 326
                                    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 5GZ1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GZ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GZ1)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 5gz1)
 
  Cis Peptide Bonds
    Asp A:124 - Pro A:125   [ RasMol ]  
    Asp B:124 - Pro B:125   [ RasMol ]  
    Gly A:149 - Lys A:150   [ RasMol ]  
    Gly B:149 - Lys B:150   [ RasMol ]  
 

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  5gz1
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  1.4.1.16
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 Related Entries

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

UniProtKB/Swiss-Prot
        DAPDH_URETH | G1UII1: 3wyb 3wyc 5gz3 5gz6

(-) Related Entries Specified in the PDB File

5gz3 5gz6