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(-) Description

Title :  STRUCTURE OF D-AMINO ACID DEHYDROGENASE IN COMPLEX WITH NADP
 
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 :  1.59
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  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , TYR A:11 , GLY A:12 , ASN A:13 , LEU A:14 , THR A:35 , ARG A:36 , ARG A:37 , CYS A:69 , GLY A:70 , GLY A:71 , SER A:72 , ASP A:75 , SER A:92 , ALA A:94 , VAL A:121 , GLY A:122 , TRP A:123 , ASP A:124 , PRO A:125 , ASN A:276 , THR A:280 , HOH A:1134 , HOH A:1145 , HOH A:1174 , HOH A:1190 , HOH A:1191binding site for residue NAP A 1001
2AC2SOFTWARETRP A:123 , TRP A:148 , GLY A:149 , GLY A:151 , VAL A:152 , ASN A:249binding site for residue EDO A 1002
3AC3SOFTWAREGLY A:149 , LYS A:150 , PRO A:248 , ASN A:272 , HOH A:1212binding site for residue EDO A 1003
4AC4SOFTWAREASN A:131 , LEU A:134 , PHE A:269 , ASN B:131 , LEU B:134 , PHE B:269binding site for residue EDO A 1004
5AC5SOFTWAREGLY B:10 , TYR B:11 , GLY B:12 , ASN B:13 , LEU B:14 , THR B:35 , ARG B:36 , ARG B:37 , CYS B:69 , GLY B:70 , GLY B:71 , SER B:72 , ASP B:75 , SER B:92 , ALA B:94 , GLY B:122 , TRP B:123 , ASP B:124 , PRO B:125 , ASN B:276 , THR B:280 , HOH B:1132 , HOH B:1139 , HOH B:1164 , HOH B:1186 , HOH B:1197 , HOH B:1200binding site for residue NAP B 1001
6AC6SOFTWAREASN B:143 , THR B:144 , TYR B:145 , HOH B:1181 , HOH B:1191binding site for residue EDO B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GZ3)

(-) 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 5GZ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GZ3)

(-) Exons   (0, 0)

(no "Exon" information available for 5GZ3)

(-) 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:325
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhh....eeeeeeee..hhhhh......eeee.hhhhhhh....eeee.....hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhh..eeeeeee..eehhhhhhhhhh...eeeeeeeeeehhhhhhhhhh......hhhhheeeeeeeee....hhhhhhhhhhh.........eeeee.hhhhhhhhh....eeeeeeeeee.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gz3 A   2 SKIRIGIVGYGNLGRGVEAAIQQNPDMELVAVFTRRDPKTVAVKSNVKVLHVDDAQSYKDEIDVMILCGGSATDLPEQGPYFAQYFNTIDSFATHARIPDYFDAVNAAAEQSGKVAIISVGWDPGLFSLNRLLGEVVLPVGNTYTFWGKGVSLGHSGAIRRIQGVKNAVQYIIPIDEAVNRVRSGENPELSTREKHAMECFVVLEEGADPAKVEHEIKTMPNFFDEYDTTVHFISEEELKQNHSGMPNGGFVIRSGKSDEGHKQIIEFSLNLESNPMFTSSALVAYARAAYRLSQNGDKGAKTVFDIPFGLLSPKSPEDLRKELL 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     


Chain B from PDB  Type:PROTEIN  Length:319
                                                                                                                                                                                                                                                                                                                                                               
               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..eehhhhhhhhh....eeeeeeeeeehhhhhhhhhh......hhhhheeeeeeeee....hhhhhhhhhhh...eeeee.hhhhhhhhh....eeeeeeeeee.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gz3 B   2 SKIRIGIVGYGNLGRGVEAAIQQNPDMELVAVFTRRDPKTVAVKSNVKVLHVDDAQSYKDEIDVMILCGGSATDLPEQGPYFAQYFNTIDSFATHARIPDYFDAVNAAAEQSGKVAIISVGWDPGLFSLNRLLGEVVLPVGNTYTFWGKGVSLGHSGAIRRIQGVKNAVQYIIPIDEAVNRVRSGENPELSTREKHAMECFVVLEEGADPAKVEHEIKTEYDTTVHFISEEELKQNHSGMPNGGFVIRSGKSDEGHKQIIEFSLNLESNPMFTSSALVAYARAAYRLSQNGDKGAKTVFDIPFGLLSPKSPEDLRKELL 326
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       227       237       247       257       267       277       287       297       307       317         
                                                                                                                                                                                                                                                    220|                                                                                                   
                                                                                                                                                                                                                                                     227
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 5GZ3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GZ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GZ3)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  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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 Related Entries

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

UniProtKB/Swiss-Prot
        DAPDH_URETH | G1UII1: 3wyb 3wyc 5gz1 5gz6

(-) Related Entries Specified in the PDB File

5gz1 5gz6