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(-) Description

Title :  YDHF, AN ALDO-KETO REDUCTASE FROM E.COLI COMPLEXED WITH NADPH
 
Authors :  S. Jeudy, C. Abergel, J. M. Claverie
Date :  24 Apr 03  (Deposition) - 29 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Oxidoreductase, Aldo-Keto Reductase, Alpha/Beta Barrel, Nadph-Dependant, Bacterial Targets At Igs-Cnrs, France, Bigs, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Jeudy, C. Abergel, J. M. Claverie
Crystal Structure Of Ydhf, An Aldo-Keto Reductase From Escherichia Coli
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL OXIDOREDUCTASE YDHF
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST17
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Other Details: THERE IS A RATIO ONE TO ONE PROTEIN MOLECULE AND NADP
    Strain: K12
    Synonym: YDHF

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1NAP3Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:20 , TRP A:22 , ARG A:23 , ASP A:50 , TYR A:55 , HIS A:128 , ARG A:129 , SER A:158 , ASN A:159 , GLN A:180 , TRP A:209 , SER A:210 , LEU A:212 , GLY A:213 , GLY A:214 , GLY A:215 , PHE A:218 , GLU A:243 , ILE A:260 , GLY A:262 , SER A:263 , GLY A:264 , LYS A:265 , ARG A:268BINDING SITE FOR RESIDUE NAP A1298
2AC2SOFTWAREGLY B:20 , TRP B:22 , ARG B:23 , ASP B:50 , TYR B:55 , HIS B:128 , ARG B:129 , SER B:158 , ASN B:159 , GLN B:180 , TRP B:209 , SER B:210 , PHE B:218 , ILE B:260 , GLY B:262 , SER B:263 , GLY B:264 , LYS B:265 , ARG B:268 , TYR C:222BINDING SITE FOR RESIDUE NAP B1299
3AC3SOFTWAREGLY C:20 , TRP C:22 , ARG C:23 , ASP C:50 , TYR C:55 , HIS C:128 , ARG C:129 , SER C:158 , ASN C:159 , GLN C:180 , TRP C:209 , SER C:210 , LEU C:212 , GLY C:213 , GLY C:214 , GLY C:215 , PHE C:218 , GLU C:243 , ILE C:260 , GLY C:262 , SER C:263 , GLY C:264 , LYS C:265 , ARG C:268BINDING SITE FOR RESIDUE NAP C1299

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OG6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OG6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OG6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OG6)

(-) Exons   (0, 0)

(no "Exon" information available for 1OG6)

(-) 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:298
 aligned with YDHF_ECOLI | P76187 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290        
           YDHF_ECOLI     1 MVQRITIAPQGPEFSRFVMGYWRLMDWNMSARQLVSFIEEHLDLGVTTVDHADIYGGYQCEAAFGEALKLAPHLRERMEIVSKCGIATTAREENVIGHYITDRDHIIKSAEQSLINLATDHLDLLLIHRPDPLMDADEVADAFKHLHQSGKVRHFGVSNFTPAQFALLQSRLPFTLATNQVEISPVHQPLLLDGTLDQLQQLRVRPMAWSCLGGGRLFNDDYFQPLRDELAVVAEELNAGSIEQVVYAWVLRLPSQPLPIIGSGKIERVRAAVEAETLKMTRQQWFRIRKAALGYDVP 298
               SCOP domains d1og6a_ A: Hypothetical oxidoreductase YdhF                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1og6A00 A:1-298 NADP-dependent oxidoreductase                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee......eee..eee..hhhhhh.hhhhhhhhhhhhh.....eee........hhhhhhhhhhhh...hhhhheeeeee.ee..........ee..hhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh........eeee.....hhhhhhhhhhhhhhhh...eee..hhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1og6 A   1 LVQRITIAPQGPEFSRFVMGYWRLMDWNMSARQLVSFIEEHLDLGVTTVDHADIYGGYQCEAAFGEALKLAPHLRERMEIVSKCGIATTAREENVIGHYITDRDHIIKSAEQSLINLATDHLDLLLIHRPDPLMDADEVADAFKHLHQSGKVRHFGVSNFTPAQFALLQSRLPFTLATNQVEISPVHQPLLLDGTLDQLQQLRVRPMAWSCLGGGRLFNDDYFQPLRDELAVVAEELNAGSIEQVVNAWVLRLPSQPLPIIGSGKIERVRAAVEAETLKMTRQQWFRIRKAALGYDVP 298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290        


Chain B from PDB  Type:PROTEIN  Length:294
 aligned with YDHF_ECOLI | P76187 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290        
           YDHF_ECOLI     1 MVQRITIAPQGPEFSRFVMGYWRLMDWNMSARQLVSFIEEHLDLGVTTVDHADIYGGYQCEAAFGEALKLAPHLRERMEIVSKCGIATTAREENVIGHYITDRDHIIKSAEQSLINLATDHLDLLLIHRPDPLMDADEVADAFKHLHQSGKVRHFGVSNFTPAQFALLQSRLPFTLATNQVEISPVHQPLLLDGTLDQLQQLRVRPMAWSCLGGGRLFNDDYFQPLRDELAVVAEELNAGSIEQVVYAWVLRLPSQPLPIIGSGKIERVRAAVEAETLKMTRQQWFRIRKAALGYDVP 298
               SCOP domains d1og6b_ B: Hypothetical oxidoreductase YdhF                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1og6B00 B:1-298 NADP-dependent oxidoreductase                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee......eee..eee..hhhhh..hhhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhh........eeeeee.ee..........ee..hhhhhhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh........ee.......hhhhhhhhhhhhhhhh........----.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhh.......ee...hhhhhhhhhh......hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1og6 B   1 LVQRITIAPQGPEFSRFVMGYWRLMDWNMSARQLVSFIEEHLDLGVTTVDHADIYGGYQCEAAFGEALKLAPHLRERMEIVSKCGIATTAREENVIGHYITDRDHIIKSAEQSLINLATDHLDLLLIHRPDPLMDADEVADAFKHLHQSGKVRHFGVSNFTPAQFALLQSRLPFTLATNQVEISPVHQPLLLDGTLDQLQQLRVRPMAWSC----RLFNDDYFQPLRDELAVVAEELNAGSIEQVVNAWVLRLPSQPLPIIGSGKIERVRAAVEAETLKMTRQQWFRIRKAALGYDVP 298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210|    | 220       230       240       250       260       270       280       290        
                                                                                                                                                                                                                                            211  216                                                                                  


Chain C from PDB  Type:PROTEIN  Length:298
 aligned with YDHF_ECOLI | P76187 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290        
           YDHF_ECOLI     1 MVQRITIAPQGPEFSRFVMGYWRLMDWNMSARQLVSFIEEHLDLGVTTVDHADIYGGYQCEAAFGEALKLAPHLRERMEIVSKCGIATTAREENVIGHYITDRDHIIKSAEQSLINLATDHLDLLLIHRPDPLMDADEVADAFKHLHQSGKVRHFGVSNFTPAQFALLQSRLPFTLATNQVEISPVHQPLLLDGTLDQLQQLRVRPMAWSCLGGGRLFNDDYFQPLRDELAVVAEELNAGSIEQVVYAWVLRLPSQPLPIIGSGKIERVRAAVEAETLKMTRQQWFRIRKAALGYDVP 298
               SCOP domains d1og6c_ C: Hypothetical oxidoreductase YdhF                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1og6C00 C:1-298 NADP-dependent oxidoreductase                                                                                                                                                                                                                                                              CATH domains
           Pfam domains (1) ---------------Aldo_ket_red-1og6C01 C:16-293                                                                                                                                                                                                                                                         ----- Pfam domains (1)
           Pfam domains (2) ---------------Aldo_ket_red-1og6C02 C:16-293                                                                                                                                                                                                                                                         ----- Pfam domains (2)
           Pfam domains (3) ---------------Aldo_ket_red-1og6C03 C:16-293                                                                                                                                                                                                                                                         ----- Pfam domains (3)
         Sec.struct. author ...eee......eee..eee..hhhhhh.hhhhhhhhhhhhhh....eee...hhhhhhhhhhhhhhhhh...hhhhheeeeee.ee..........ee..hhhhhhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhh........eeee.....hhhhh.hhhhhhhhh....eee..hhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1og6 C   1 LVQRITIAPQGPEFSRFVMGYWRLMDWNMSARQLVSFIEEHLDLGVTTVDHADIYGGYQCEAAFGEALKLAPHLRERMEIVSKCGIATTAREENVIGHYITDRDHIIKSAEQSLINLATDHLDLLLIHRPDPLMDADEVADAFKHLHQSGKVRHFGVSNFTPAQFALLQSRLPFTLATNQVEISPVHQPLLLDGTLDQLQQLRVRPMAWSCLGGGRLFNDDYFQPLRDELAVVAEELNAGSIEQVVNAWVLRLPSQPLPIIGSGKIERVRAAVEAETLKMTRQQWFRIRKAALGYDVP 298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Aldo_ket_red] (94)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (YDHF_ECOLI | P76187)
molecular function
    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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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UniProtKB/Swiss-Prot
        YDHF_ECOLI | P76187: 1ur3

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