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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE OXIDOREDUCTASE FROM PSEUDOMONAS PUTIDA KT2440
 
Authors :  V. N. Malashkevich, Y. Patskovsky, R. Toro, J. M. Sauder, S. K. Burley, S New York Sgx Research Center For Structural Genomics (Nysgx
Date :  23 Dec 09  (Deposition) - 12 Jan 10  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Protein Structure Initiative, Oxidoreductase, Psi-2, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, Y. Patskovsky, R. Toro, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Putative Oxidoreductase From Pseudomonas Putida Kt2440
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE OXIDOREDUCTASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NP_744942.1, PP2798
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 160488
    Strain: KT2440

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3L6D)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L6D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L6D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L6D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L6D)

(-) Exons   (0, 0)

(no "Exon" information available for 3L6D)

(-) 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:293
 aligned with Q88J51_PSEPK | Q88J51 from UniProtKB/TrEMBL  Length:302

    Alignment length:293
                                    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       282       292   
         Q88J51_PSEPK     3 EHSDESFEFDVSVIGLGAMGTIMAQVLLKQGKRVAIWNRSPGKAAALVAAGAHLCESVKAALSASPATIFVLLDNHATHEVLGMPGVARALAHRTIVDYTTNAQDEGLALQGLVNQAGGHYVKGMIVAYPRNVGHRESHSIHTGDREAFEQHRALLEGLAGHTVFLPWDEALAFATVLHAHAFAAMVTFFEAVGAGDRFGLPVSKTARLLLETSRFFVADALEEAVRRLETQDFKGDQARLDVHADAFAHIAQSLHAQGVWTPVFDAVCQVVQRAAAMGYGDQDIAATTKSFA 295
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee..hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh.ee..hhhhhhhhh.eeee...hhhhhhhhhh..hhhhhh...eeee......hhhhhhhhhhhhh..eeeeeeee.hhhhh.....eeeeeehhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l6d A   2 SLSDESFEFDVSVIGLGAmGTImAQVLLKQGKRVAIWNRSPGKAAALVAAGAHLCESVKAALSASPATIFVLLDNHATHEVLGmPGVARALAHRTIVDYTTNAQDEGLALQGLVNQAGGHYVKGmIVAYPRNVGHRESHSIHTGDREAFEQHRALLEGLAGHTVFLPWDEALAFATVLHAHAFAAmVTFFEAVGAGDRFGLPVSKTARLLLETSRFFVADALEEAVRRLETQDFKGDQARLDVHADAFAHIAQSLHAQGVWTPVFDAVCQVVQRAAAmGYGDQDIAATTKSFA 294
                                    11        21  |     31        41        51        61        71        81   |    91       101       111       121    |  131       141       151       161       171       181     | 191       201       211       221       231       241       251       261       271       281       291   
                                             20-MSE                                                           85-MSE                                  126-MSE                                                      187-MSE                                                                                     279-MSE           
                                                 24-MSE                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:295
 aligned with Q88J51_PSEPK | Q88J51 from UniProtKB/TrEMBL  Length:302

    Alignment length:295
                                    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       282       292     
         Q88J51_PSEPK     3 EHSDESFEFDVSVIGLGAMGTIMAQVLLKQGKRVAIWNRSPGKAAALVAAGAHLCESVKAALSASPATIFVLLDNHATHEVLGMPGVARALAHRTIVDYTTNAQDEGLALQGLVNQAGGHYVKGMIVAYPRNVGHRESHSIHTGDREAFEQHRALLEGLAGHTVFLPWDEALAFATVLHAHAFAAMVTFFEAVGAGDRFGLPVSKTARLLLETSRFFVADALEEAVRRLETQDFKGDQARLDVHADAFAHIAQSLHAQGVWTPVFDAVCQVVQRAAAMGYGDQDIAATTKSFARE 297
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------NAD_binding_2-3l6dB01 B:9-168                                                                                                                                   -------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------NAD_binding_2-3l6dB02 B:9-168                                                                                                                                   -------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhh...eeee..hhhhhhhhhhhhhh...eeee..hhhhhhhhhhh..ee..hhhhhhhhh.eeee...hhhhhhhhhhh.hhhhhhh..eeee....hhhhhhhhhhhhhhh..eeeeeeee.hhhhh.....eeeeeehhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l6d B   2 SLSDESFEFDVSVIGLGAmGTImAQVLLKQGKRVAIWNRSPGKAAALVAAGAHLCESVKAALSASPATIFVLLDNHATHEVLGmPGVARALAHRTIVDYTTNAQDEGLALQGLVNQAGGHYVKGmIVAYPRNVGHRESHSIHTGDREAFEQHRALLEGLAGHTVFLPWDEALAFATVLHAHAFAAmVTFFEAVGAGDRFGLPVSKTARLLLETSRFFVADALEEAVRRLETQDFKGDQARLDVHADAFAHIAQSLHAQGVWTPVFDAVCQVVQRAAAmGYGDQDIAATTKSFARE 296
                                    11        21  |     31        41        51        61        71        81   |    91       101       111       121    |  131       141       151       161       171       181     | 191       201       211       221       231       241       251       261       271       281       291     
                                             20-MSE                                                           85-MSE                                  126-MSE                                                      187-MSE                                                                                     279-MSE             
                                                 24-MSE
   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 3L6D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L6D)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q88J51_PSEPK | Q88J51)
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.
    GO:0004616    phosphogluconate dehydrogenase (decarboxylating) activity    Catalysis of the reaction: 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH + H+.
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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