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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-QUINUCLIDINONE REDUCTASE FROM AGROBACTERIUM TUMEFACIENS
 
Authors :  F. Hou, T. Miyakawa, M. Tanokura
Date :  22 Jun 13  (Deposition) - 25 Jun 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Sdr, 3-Quinuclidinone, Rossmann Fold, Carbonyl Reductase, Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Hou, T. Miyakawa, M. Kataoka, D. Takeshita, S. Kumashiro, K. Nagata S. Shimizu, M. Tanokura
Structural Basis For High Substrate-Binding Affinity Of 3-Quinuclidinone Reductase Atqr
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NADH-DEPENDENT QUINUCLIDINONE REDUCTASE
    Chains: A, B, D, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: AGROBACTERIUM TUMEFACIENS
    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  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
3NAD3Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER 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 , ALA A:91 , GLY A:92 , THR A:141 , ALA A:142 , SER A:143 , TYR A:156 , LYS A:160 , PRO A:186 , GLY A:187 , VAL A:189 , THR A:191 , MET A:193 , ARG A:196 , HOH A:409 , HOH A:419 , HOH A:431 , HOH A:484 , HOH A:485 , HOH A:503 , HOH A:509BINDING SITE FOR RESIDUE NAD A 301
2AC2SOFTWAREASN A:252 , VAL A:253 , THR A:254 , GLY A:255 , GLY A:256 , ARG A:258 , PHE B:245 , MET B:246 , THR B:247 , GLN B:249BINDING SITE FOR RESIDUE ACY A 302
3AC3SOFTWAREGLU A:61 , SER A:69 , HOH A:454BINDING SITE FOR RESIDUE EDO A 303
4AC4SOFTWAREGLY B:16 , SER B:18 , 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 , ALA B:91 , 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:410 , HOH B:433 , HOH B:489BINDING SITE FOR RESIDUE NAD B 301
5AC5SOFTWAREPHE A:245 , MET A:246 , THR A:247 , GLN A:249 , ASN B:252 , VAL B:253 , THR B:254 , GLY B:255 , GLY B:256BINDING SITE FOR RESIDUE ACY B 302
6AC6SOFTWAREPHE C:245 , MET C:246 , THR C:247 , GLN C:249 , ASN D:252 , VAL D:253 , THR D:254 , GLY D:255 , GLY D:256 , ARG D:258BINDING SITE FOR RESIDUE ACY D 301
7AC7SOFTWAREGLY 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 , GLY C:187 , VAL C:189 , THR C:191 , MET C:193 , ARG C:196 , HOH C:404 , HOH C:468 , HOH C:481 , HOH C:484 , HOH C:486 , HOH C:554BINDING SITE FOR RESIDUE NAD C 301
8AC8SOFTWAREASN C:252 , VAL C:253 , THR C:254 , GLY C:255 , GLY C:256 , ARG C:258 , PHE D:245 , MET D:246 , THR D:247 , GLN D:249BINDING SITE FOR RESIDUE ACY C 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WDS)

(-) 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:257
 aligned with G1K3P5_RHIRD | G1K3P5 from UniProtKB/TrEMBL  Length:263

    Alignment length:257
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       
         G1K3P5_RHIRD     7 IFDLSGRKAIVTGGSKGIGAAIARALDKAGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANAGVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNTKGVIVNTASLAAKVGAPLLAHYSASKFAVFGWTQALAREMAPKNIRVNCVCPGFVKTAMQEREIIWEAELRGMTPEAVRAEYVSLTPLGRIEEPEDVADVVVFLASDAARFMTGQGINVTGGVRMD 263
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wds A   4 IFDLSGRKAIVTGGSKGIGAAIARALDKAGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANAGVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNTKGVIVNTASLAAKVGAPLLAHYSASKFAVFGWTQALAREMAPKNIRVNCVCPGFVKTAMQEREIIWEAELRGMTPEAVRAEYVSLTPLGRIEEPEDVADVVVFLASDAARFMTGQGINVTGGVRMD 260
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       


Chain B from PDB  Type:PROTEIN  Length:257
 aligned with G1K3P5_RHIRD | G1K3P5 from UniProtKB/TrEMBL  Length:263

    Alignment length:257
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       
         G1K3P5_RHIRD     7 IFDLSGRKAIVTGGSKGIGAAIARALDKAGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANAGVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNTKGVIVNTASLAAKVGAPLLAHYSASKFAVFGWTQALAREMAPKNIRVNCVCPGFVKTAMQEREIIWEAELRGMTPEAVRAEYVSLTPLGRIEEPEDVADVVVFLASDAARFMTGQGINVTGGVRMD 263
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wds B   4 IFDLSGRKAIVTGGSKGIGAAIARALDKAGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANAGVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNTKGVIVNTASLAAKVGAPLLAHYSASKFAVFGWTQALAREMAPKNIRVNCVCPGFVKTAMQEREIIWEAELRGMTPEAVRAEYVSLTPLGRIEEPEDVADVVVFLASDAARFMTGQGINVTGGVRMD 260
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       


Chain C from PDB  Type:PROTEIN  Length:257
 aligned with G1K3P5_RHIRD | G1K3P5 from UniProtKB/TrEMBL  Length:263

    Alignment length:257
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       
         G1K3P5_RHIRD     7 IFDLSGRKAIVTGGSKGIGAAIARALDKAGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANAGVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNTKGVIVNTASLAAKVGAPLLAHYSASKFAVFGWTQALAREMAPKNIRVNCVCPGFVKTAMQEREIIWEAELRGMTPEAVRAEYVSLTPLGRIEEPEDVADVVVFLASDAARFMTGQGINVTGGVRMD 263
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 3wds C   4 IFDLSGRKAIVTGGSKGIGAAIARALDKAGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANAGVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNTKGVIVNTASLAAKVGAPLLAHYSASKFAVFGWTQALAREMAPKNIRVNCVCPGFVKTAMQEREIIWEAELRGMTPEAVRAEYVSLTPLGRIEEPEDVADVVVFLASDAARFMTGQGINVTGGVRMD 260
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       


Chain D from PDB  Type:PROTEIN  Length:257
 aligned with G1K3P5_RHIRD | G1K3P5 from UniProtKB/TrEMBL  Length:263

    Alignment length:257
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       
         G1K3P5_RHIRD     7 IFDLSGRKAIVTGGSKGIGAAIARALDKAGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANAGVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNTKGVIVNTASLAAKVGAPLLAHYSASKFAVFGWTQALAREMAPKNIRVNCVCPGFVKTAMQEREIIWEAELRGMTPEAVRAEYVSLTPLGRIEEPEDVADVVVFLASDAARFMTGQGINVTGGVRMD 263
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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......hhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wds D   4 IFDLSGRKAIVTGGSKGIGAAIARALDKAGATVAIADLDVMAAQAVVAGLENGGFAVEVDVTKRASVDAAMQKAIDALGGFDLLCANAGVSTMRPAVDITDEEWDFNFDVNARGVFLANQIACRHFLASNTKGVIVNTASLAAKVGAPLLAHYSASKFAVFGWTQALAREMAPKNIRVNCVCPGFVKTAMQEREIIWEAELRGMTPEAVRAEYVSLTPLGRIEEPEDVADVVVFLASDAARFMTGQGINVTGGVRMD 260
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253
   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 3WDS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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 Related Entries

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

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        G1K3P5_RHIRD | G1K3P5: 3ak4

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