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(-) Description

Title :  CRYSTAL STRUCTURE OF NADH-DEPENDENT QUINUCLIDINONE REDUCTASE FROM AGROBACTERIUM TUMEFACIENS
 
Authors :  T. Miyakawa, M. Kataoka, D. Takeshita, F. Nomoto, K. Nagata, S. Shimizu M. Tanokura
Date :  07 Jul 10  (Deposition) - 13 Jul 11  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Sdr, 3-Quinuclidinone, (R)-3-Quinuclidinol, Chiral Alcohol, Carbonyl Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Miyakawa, M. Kataoka, D. Takeshita, F. Nomoto, K. Nagata, S. Shimizu, M. Tanokura
Crystal Structure Of Nadh-Dependent Quinuclidinone Reductas From Agrobacterium Tumefaciens
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NADH-DEPENDENT QUINUCLIDINONE REDUCTASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PRASMID
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 358

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:16 , SER A:18 , LYS A:19 , GLY A:20 , ILE A:21 , ASP A:40 , LEU A:41 , VAL A:62 , ASP A:63 , VAL A:64 , ASN A:90 , GLY A:92 , THR A:141 , ALA A:142 , SER A:143 , TYR A:156 , LYS A:160 , GLY A:187 , VAL A:189 , THR A:191 , MET A:193 , ARG A:196 , HOH A:276 , HOH A:281 , HOH A:283 , HOH A:291 , HOH A:301 , HOH A:413BINDING SITE FOR RESIDUE NAD A 901
2AC2SOFTWAREGLY B:16 , LYS B:19 , GLY B:20 , ILE B:21 , ASP B:40 , LEU B:41 , VAL B:62 , ASP B:63 , VAL B:64 , ASN B:90 , GLY B:92 , THR B:141 , ALA B:142 , SER B:143 , TYR B:156 , LYS B:160 , PRO B:186 , GLY B:187 , VAL B:189 , THR B:191 , MET B:193 , ARG B:196 , HOH B:282 , HOH B:310 , HOH B:333 , HOH B:347 , HOH B:404BINDING SITE FOR RESIDUE NAD B 902
3AC3SOFTWAREGLY C:16 , SER C:18 , LYS C:19 , GLY C:20 , ILE C:21 , ASP C:40 , LEU C:41 , VAL C:62 , ASP C:63 , VAL C:64 , ASN C:90 , ALA C:91 , GLY C:92 , THR C:141 , ALA C:142 , SER C:143 , TYR C:156 , LYS C:160 , PRO C:186 , GLY C:187 , VAL C:189 , THR C:191 , MET C:193 , ARG C:196 , HOH C:267 , HOH C:271 , HOH C:274 , HOH C:299 , HOH C:302 , HOH C:311 , HOH C:490BINDING SITE FOR RESIDUE NAD C 903
4AC4SOFTWAREGLY D:16 , SER D:18 , LYS D:19 , GLY D:20 , ILE D:21 , ASP D:40 , LEU D:41 , VAL D:62 , ASP D:63 , VAL D:64 , ASN D:90 , ALA D:91 , GLY D:92 , THR D:141 , ALA D:142 , SER D:143 , TYR D:156 , LYS D:160 , PRO D:186 , GLY D:187 , VAL D:189 , THR D:191 , MET D:193 , ARG D:196 , HOH D:280 , HOH D:289 , HOH D:304 , HOH D:390 , HOH D:661BINDING SITE FOR RESIDUE NAD D 904

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AK4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3AK4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AK4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AK4)

(-) Exons   (0, 0)

(no "Exon" information available for 3AK4)

(-) 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:258
 aligned with G1K3P5_RHIRD | G1K3P5 from UniProtKB/TrEMBL  Length:263

    Alignment length:258
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255        
         G1K3P5_RHIRD     6 GIFDLSGRKAIVTGGSKGIGAAIARALDKAGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANAGVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNTKGVIVNTASLAAKVGAPLLAHYSASKFAVFGWTQALAREMAPKNIRVNCVCPGFVKTAMQEREIIWEAELRGMTPEAVRAEYVSLTPLGRIEEPEDVADVVVFLASDAARFMTGQGINVTGGVRMD 263
               SCOP domains d3ak4a_ A: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ak4 A   3 GIFDLSGRKAIVTGGSKGIGAAIARALDKAGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANAGVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNTKGVIVNTASLAAKVGAPLLAHYSASKFAVFGWTQALAREMAPKNIRVNCVCPGFVKTAMQEREIIWEAELRGMTPEAVRAEYVSLTPLGRIEEPEDVADVVVFLASDAARFMTGQGINVTGGVRMD 260
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252        


Chain B from PDB  Type:PROTEIN  Length:258
 aligned with G1K3P5_RHIRD | G1K3P5 from UniProtKB/TrEMBL  Length:263

    Alignment length:258
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255        
         G1K3P5_RHIRD     6 GIFDLSGRKAIVTGGSKGIGAAIARALDKAGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANAGVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNTKGVIVNTASLAAKVGAPLLAHYSASKFAVFGWTQALAREMAPKNIRVNCVCPGFVKTAMQEREIIWEAELRGMTPEAVRAEYVSLTPLGRIEEPEDVADVVVFLASDAARFMTGQGINVTGGVRMD 263
               SCOP domains d3ak4b_ B: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ak4 B   3 GIFDLSGRKAIVTGGSKGIGAAIARALDKAGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANAGVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNTKGVIVNTASLAAKVGAPLLAHYSASKFAVFGWTQALAREMAPKNIRVNCVCPGFVKTAMQEREIIWEAELRGMTPEAVRAEYVSLTPLGRIEEPEDVADVVVFLASDAARFMTGQGINVTGGVRMD 260
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252        


Chain C from PDB  Type:PROTEIN  Length:258
 aligned with G1K3P5_RHIRD | G1K3P5 from UniProtKB/TrEMBL  Length:263

    Alignment length:258
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255        
         G1K3P5_RHIRD     6 GIFDLSGRKAIVTGGSKGIGAAIARALDKAGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANAGVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNTKGVIVNTASLAAKVGAPLLAHYSASKFAVFGWTQALAREMAPKNIRVNCVCPGFVKTAMQEREIIWEAELRGMTPEAVRAEYVSLTPLGRIEEPEDVADVVVFLASDAARFMTGQGINVTGGVRMD 263
               SCOP domains d3ak4c_ C: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ak4 C   3 GIFDLSGRKAIVTGGSKGIGAAIARALDKAGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANAGVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNTKGVIVNTASLAAKVGAPLLAHYSASKFAVFGWTQALAREMAPKNIRVNCVCPGFVKTAMQEREIIWEAELRGMTPEAVRAEYVSLTPLGRIEEPEDVADVVVFLASDAARFMTGQGINVTGGVRMD 260
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252        


Chain D from PDB  Type:PROTEIN  Length:258
 aligned with G1K3P5_RHIRD | G1K3P5 from UniProtKB/TrEMBL  Length:263

    Alignment length:258
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255        
         G1K3P5_RHIRD     6 GIFDLSGRKAIVTGGSKGIGAAIARALDKAGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANAGVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNTKGVIVNTASLAAKVGAPLLAHYSASKFAVFGWTQALAREMAPKNIRVNCVCPGFVKTAMQEREIIWEAELRGMTPEAVRAEYVSLTPLGRIEEPEDVADVVVFLASDAARFMTGQGINVTGGVRMD 263
               SCOP domains d3ak4d_ D: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ak4 D   3 GIFDLSGRKAIVTGGSKGIGAAIARALDKAGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANAGVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNTKGVIVNTASLAAKVGAPLLAHYSASKFAVFGWTQALAREMAPKNIRVNCVCPGFVKTAMQEREIIWEAELRGMTPEAVRAEYVSLTPLGRIEEPEDVADVVVFLASDAARFMTGQGINVTGGVRMD 260
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AK4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AK4)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (G1K3P5_RHIRD | G1K3P5)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.
biological process
    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.

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        G1K3P5_RHIRD | G1K3P5: 3wds

(-) Related Entries Specified in the PDB File

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