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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE TROPINONE REDUCTASE-II FROM CAENORHABDITIS ELEGANS WITH COFACTOR AND SUBSTRATE
 
Authors :  N. Schormann, E. Karpova, J. Zhou, Y. Zhang, J. Symersky, R. Bunzel, W. - A. Arabshahi, S. Qiu, C. -H. Luan, R. Gray, M. Carson, J. Tsao, M. Luo, D. S. Lu, G. Lin, D. Luo, Z. Cao, S. Li, A. Mckinstry, Q. Shang, Y. -J. Chen, T L. Nagy, L. Delucas, Southeast Collaboratory For Structural Gen (Secsg)
Date :  20 Sep 04  (Deposition) - 28 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Parallel Beta-Sheet Of Seven Strands In The Order 3214567, Three Alpha-Helices On Either Side Of Beta-Sheet, Seventh Alpha-Helix On Top Of Beta-Sheet, Structural Genomics, Protein Structure Initiative, Scsg, Psi, Southeast Collaboratory For Structural Genomics, Secsg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Schormann, E. Karpova, J. Zhou, Y. Zhang, J. Symersky, R. Bunzel, W. -Y. Huang, A. Arabshahi, S. Qiu, C. -H. Luan, R. Gray, M. Carson, J. Tsao, M. Luo, D. Johnson, S. Lu, G. Lin, D. Luo, Z. Cao, S. Li, A. Mckinstry, Q. Shang, Y. -J. Chen, T. Bray, L. Nagy, L. Delucas
Crystal Structure Of Putative Tropinone Reductase-Ii From Caenorhabditis Elegans With Cofactor And Substrate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SHORT-CHAIN DEHYDROGENASE/REDUCTASE FAMILY MEMBER (5L265), PUTATIVE TROPINONE REDUCTASE-II
    Chains: A, B
    EC Number: 1.1.1.236
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: F25D1.5
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2TNE2Ligand/Ion8-METHYL-8-AZABICYCLO[3,2,1]OCTAN-3-ONE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2TNE4Ligand/Ion8-METHYL-8-AZABICYCLO[3,2,1]OCTAN-3-ONE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , SER A:14 , SER A:15 , ASN A:16 , GLY A:17 , ILE A:18 , GLY A:37 , ARG A:38 , ASN A:39 , ARG A:42 , ALA A:65 , ASP A:66 , VAL A:67 , ASN A:93 , ALA A:94 , GLY A:95 , LEU A:118 , SER A:145 , SER A:146 , TYR A:160 , LYS A:164 , PRO A:190 , GLY A:191 , ALA A:192 , VAL A:193 , THR A:195 , GLY A:196 , PHE A:197 , TNE A:1279 , HOH A:1291 , HOH A:1316 , HOH A:1322 , HOH A:1325BINDING SITE FOR RESIDUE NDP A 1278
2AC2SOFTWAREGLY B:13 , SER B:14 , SER B:15 , ASN B:16 , GLY B:17 , ILE B:18 , GLY B:37 , ARG B:38 , ASN B:39 , ARG B:42 , ALA B:65 , ASP B:66 , VAL B:67 , ASN B:93 , ALA B:94 , GLY B:95 , LEU B:118 , VAL B:144 , SER B:145 , SER B:146 , TYR B:160 , LYS B:164 , PRO B:190 , GLY B:191 , ALA B:192 , VAL B:193 , THR B:195 , GLY B:196 , PHE B:197 , TNE B:2279 , HOH B:2280 , HOH B:2282 , HOH B:2291 , HOH B:2311 , HOH B:2317 , HOH B:2385BINDING SITE FOR RESIDUE NDP B 2278
3AC3SOFTWARETYR A:157 , GLY A:191 , NDP A:1278 , HOH A:1280 , HOH A:1368BINDING SITE FOR RESIDUE TNE A 1279
4AC4SOFTWARETYR B:157 , ALA B:192 , PHE B:197 , NDP B:2278BINDING SITE FOR RESIDUE TNE B 2279

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XHL)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:150 -Pro A:151
2Gly B:150 -Pro B:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XHL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XHL)

(-) Exons   (0, 0)

(no "Exon" information available for 1XHL)

(-) Sequences/Alignments

Asymmetric 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:274
 aligned with Q19774_CAEEL | Q19774 from UniProtKB/TrEMBL  Length:277

    Alignment length:274
                                    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       262       272    
         Q19774_CAEEL     3 RFSGKSVIITGSSNGIGRSAAVIFAKEGAQVTITGRNEDRLEETKQQILKAGVPAEKINAVVADVTEASGQDDIINTTLAKFGKIDILVNNAGANLADGTANTDQPVELYQKTFKLNFQAVIEMTQKTKEHLIKTKGEIVNVSSIVAGPQAHSGYPYYACAKAALDQYTRCTAIDLIQHGVRVNSVSPGAVATGFMGAMGLPETASDKLYSFIGSRKECIPVGHCGKPEEIANIIVFLADRNLSSYIIGQSIVADGGSTLVMGMQTHDLMSVLS 276
               SCOP domains d1xhla_ A: Hypothetical protein F25D1.5                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1xhlA00 A:3-276 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhh..hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xhl A   3 RFSGKSVIITGSSNGIGRSAAVIFAKEGAQVTITGRNEDRLEETKQQILKAGVPAEKINAVVADVTEASGQDDIINTTLAKFGKIDILVNNAGANLADGTANTDQPVELYQKTFKLNFQAVIEMTQKTKEHLIKTKGEIVNVSSIVAGPQAHSGYPYYACAKAALDQYTRCTAIDLIQHGVRVNSVSPGAVATGFMGAMGLPETASDKLYSFIGSRKECIPVGHCGKPEEIANIIVFLADRNLSSYIIGQSIVADGGSTLVMGMQTHDLMSVLS 276
                                    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       262       272    


Chain B from PDB  Type:PROTEIN  Length:274
 aligned with Q19774_CAEEL | Q19774 from UniProtKB/TrEMBL  Length:277

    Alignment length:274
                                    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       262       272    
         Q19774_CAEEL     3 RFSGKSVIITGSSNGIGRSAAVIFAKEGAQVTITGRNEDRLEETKQQILKAGVPAEKINAVVADVTEASGQDDIINTTLAKFGKIDILVNNAGANLADGTANTDQPVELYQKTFKLNFQAVIEMTQKTKEHLIKTKGEIVNVSSIVAGPQAHSGYPYYACAKAALDQYTRCTAIDLIQHGVRVNSVSPGAVATGFMGAMGLPETASDKLYSFIGSRKECIPVGHCGKPEEIANIIVFLADRNLSSYIIGQSIVADGGSTLVMGMQTHDLMSVLS 276
               SCOP domains d1xhlb_ B: Hypothetical protein F25D1.5                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1xhlB00 B:3-276 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) ---------adh_short_C2-1xhlB01 B:12-261                                                                                                                                                                                                                             --------------- Pfam domains (1)
           Pfam domains (2) ---------adh_short_C2-1xhlB02 B:12-261                                                                                                                                                                                                                             --------------- Pfam domains (2)
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhh..hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xhl B   3 RFSGKSVIITGSSNGIGRSAAVIFAKEGAQVTITGRNEDRLEETKQQILKAGVPAEKINAVVADVTEASGQDDIINTTLAKFGKIDILVNNAGANLADGTANTDQPVELYQKTFKLNFQAVIEMTQKTKEHLIKTKGEIVNVSSIVAGPQAHSGYPYYACAKAALDQYTRCTAIDLIQHGVRVNSVSPGAVATGFMGAMGLPETASDKLYSFIGSRKECIPVGHCGKPEEIANIIVFLADRNLSSYIIGQSIVADGGSTLVMGMQTHDLMSVLS 276
                                    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       262       272
   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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q19774_CAEEL | Q19774)
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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  1xhl
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  Q19774_CAEEL | Q19774
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  1.1.1.236
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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1XHL)

(-) Related Entries Specified in the PDB File

1ipf TROPINONE REDUCTASE-II FROM DATURA STRAMONIUM WITH COFACTOR AND SUBSTRATE. RELATED ID: F25D1.5 RELATED DB: TARGETDB
1ooe A C. ELEGANS PROTEIN (DIHYDROPTERIDINE REDUCTASE) FROM THE SAME FAMILY (SDR FAMILY).
1spx A C. ELEGANS PROTEIN (PUTATIVE GLUCOSE DEHYDROGENASE) FROM THE SAME FAMILY (SDR FAMILY).