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(-) Description

Title :  STRUCTURE OF D-AMINO ACID DEHYDROGENASE IN COMPLEX WITH NADPH AND 2-KETO-6-AMINOCAPRONIC ACID
 
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 :  1.74
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  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
17C31Ligand/Ion6-AZANYL-2-OXIDANYLIDENE-HEXANOIC ACID
2ACT1Ligand/IonACETATE ION
3NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
4SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
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 , THR A:280 , 7C3 A:1002 , HOH A:1101 , HOH A:1128 , HOH A:1138 , HOH A:1253 , ARG B:37 , THR B:41 , HOH B:3101binding site for residue NDP A 1001
2AC2SOFTWAREASP A:124 , TRP A:148 , LYS A:150 , NDP A:1001 , HOH A:1106binding site for residue 7C3 A 1002
3AC3SOFTWAREASN A:249 , LEU A:273 , ASN A:276 , PRO A:277 , MET A:278 , PHE A:279 , HOH A:1251binding site for residue SO4 A 1003
4AC4SOFTWARELEU A:130 , ASN A:131 , LEU B:127 , ASN B:131 , PHE B:310 , HOH B:3105binding site for residue ACT B 3001
5AC5SOFTWAREARG A:37 , ASP A:38 , GLY B:12 , ARG B:16binding site for residue SO4 B 3002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GZ6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:124 -Pro A:125
2Asp B:124 -Pro B:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GZ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GZ6)

(-) Exons   (0, 0)

(no "Exon" information available for 5GZ6)

(-) 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:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhh....eeeeeeee..hhhhh......eeee.hhhhhhh....eeee.....hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhh..eeeeeeeeee.....hhhhh..eeeeeeeeeehhhhhhhhhhh.....hhhhheeeeeeeee....hhhhhhhhhhhh........eeeee.hhhhhhhhh....eeeeeeeee..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5gz6 A   2 SKIRIGIVGYGNLGRGVEAAIQQNPDMELVAVFTRRDPKTVAVKSNVKVLHVDDAQSYKDEIDVMILCGGSATDLPEQGPYFAQYFNTIDSFATHARIPDYFDAVNAAAEQSGKVAIISVGWDPGLFSLNRLLGEVVLPVGNTYTFWGKGVSLGGAIRRIQGVKNAVQYIIPIDEAVNRVRSGENPELSTREKHAMECFVVLEEGADPAKVEHEIKTMPNFFDEYDTTVHFISEEELKQNHSGMPNGGFVIRSGKKQIIEFSLNLESNPMFTSSALVAYARAAYRLSQNGDKGAKTVFDIPFGLLSPKSPEDLRKELL 326
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   ||  163       173       183       193       203       213       223       233       243       253    || 268       278       288       298       308       318        
                                                                                                                                                                                   155|                                                                                                 258|                                                              
                                                                                                                                                                                    158                                                                                                  264                                                              


Chain B from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhh....eeeeeeee..hhhhh......eeee.hhhhhhh....eeee.....hhhhhhhhhhhhhh.ee....hhhhhhhhhhhhhhhhhhhh.eee.......hhhhhhhhhhhhhh..eeeeeeeeeee....hhhhh..eeeeeeeeeehhhhhhhhhh......hhhhheeeeeeeee....hhhhhhhhhhh.........eeeee.hhhhhhhhh..eeeeeeeee...eeeeeeeee...hhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gz6 B   2 SKIRIGIVGYGNLGRGVEAAIQQNPDMELVAVFTRRDPKTVAVKSNVKVLHVDDAQSYKDEIDVMILCGGSATDLPEQGPYFAQYFNTIDSFATHARIPDYFDAVNAAAEQSGKVAIISVGWDPGLFSLNRLLGEVVLPVGNTYTFWGKGVSLGGAIRRIQGVKNAVQYIIPIDEAVNRVRSGENPELSTREKHAMECFVVLEEGADPAKVEHEIKTMPNFFDEYDTTVHFISEEELKQNHMPNGGFVIRSGKKQIIEFSLNLESNPMFTSSALVAYARAAYRLSQNGDKGAKTVFDIPFGLLSPKSPEDLRKELL 326
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   ||  163       173       183       193       203       213       223       233       243||     255  ||   270       280       290       300       310       320      
                                                                                                                                                                                   155|                                                                                   244|        258|                                                              
                                                                                                                                                                                    158                                                                                    247         264
   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 5GZ6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GZ6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GZ6)

(-) 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 ]  
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  5gz6
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  DAPDH_URETH | G1UII1
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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 5gz1 5gz3

(-) Related Entries Specified in the PDB File

5gz1 5gz3