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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE 15-KETOPROSTAGLANDIN DELTA-13-REDUCTASE IN COMPLEX WITH NADPH
 
Authors :  Y. H. Wu, A. H. J. Wang, T. P. Ko, R. T. Guo, S. M. Hu, L. M. Chuang
Date :  16 Oct 07  (Deposition) - 30 Sep 08  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. H. Wu, T. P. Ko, R. T. Guo, S. M. Hu, L. M. Chuang, A. H. J. Wang
Structural Basis For Catalytic And Inhibitory Mechanisms Of Human Prostaglandin Reductase Ptgr2.
Structure V. 16 1714 2008
PubMed-ID: 19000823  |  Reference-DOI: 10.1016/J.STR.2008.09.007
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROSTAGLANDIN REDUCTASE 2
    Chains: A
    EC Number: 1.3.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX4T
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PTGR2, ZADH1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: PTGR2, 15-OXOPROSTAGLANDIN 13-REDUCTASE, ZINC- BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:50 , MET A:135 , THR A:139 , GLY A:165 , ALA A:166 , CYS A:167 , CYS A:187 , GLY A:188 , LYS A:192 , TYR A:208 , ASN A:231 , VAL A:232 , CYS A:253 , GLY A:254 , GLN A:255 , ILE A:256 , TYR A:259 , PHE A:287 , VAL A:289 , MET A:332 , MET A:333 , GLY A:335 , ASN A:337 , GLY A:339 , HOH A:435 , HOH A:452 , HOH A:453 , HOH A:457 , HOH A:458 , HOH A:464 , HOH A:465 , HOH A:466 , HOH A:467 , HOH A:546 , HOH A:560 , HOH A:611BINDING SITE FOR RESIDUE NDP A 900

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZB3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZB3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZB3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZB3)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZB3)

(-) 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:345
 aligned with PTGR2_MOUSE | Q8VDQ1 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:345
                                    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       301       311       321       331       341     
          PTGR2_MOUSE     2 IIQRVVLNSRPGKNGNPVAENFRVEEFSLPDALNEGQVQVRTLYLSVDPYMRCKMNEDTGTDYLAPWQLAQVADGGGIGVVEESKHQKLTKGDFVTSFYWPWQTKAILDGNGLEKVDPQLVDGHLSYFLGAIGMPGLTSLIGVQEKGHISAGSNQTMVVSGAAGACGSLAGQIGHLLGCSRVVGICGTQEKCLFLTSELGFDAAVNYKTGNVAEQLREACPGGVDVYFDNVGGDISNAVISQMNENSHIILCGQISQYSNDVPYPPPLPPAVEAIRKERNITRERFTVLNYKDKFEPGILQLSQWFKEGKLKVKETMAKGLENMGVAFQSMMTGGNVGKQIVCIS 346
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------2zb3A02 A:133-313 NAD(P)-binding Rossmann-like Domain                                                                                                                                --------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_zinc_N-2zb3A01 A:166-283                                                                                          --------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..........hhh.eeeeee.........eeeeeeeeee..hhhhhhh..................eeeeeeeeeee.........eeeeeeee...eeeee.hhhee.hhhhhh.hhhhhhh..hhhhhhhhhhhhhhh........eeeee...hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh....eeee.hhhhhhhhhhhhh...eeeeee..hhhhhhhhhhheeeeeeeee..hhhhh..........hhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhh.....eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zb3 A   2 IIQRVVLNSRPGKNGNTVAENFRVEEFSLPDALNEGQVQVRTLYLSVDPYMRCKMNEDTGTDYLAPWQLAQVADGGGIGVVEESKHQKLTKGDFVTSFYWPWQTKAILDGNGLEKVDPQLVDGHLSYFLGAIGMPGLTSLIGVQEKGHISAGSNQTMVVSGAAGACGSLAGQIGHLLGCSRVVGICGTQEKCLFLTSELGFDAAVNYKTGNVAEQLREACPGGVDVYFDNVGGDISNAVISQMNENSHIILCGQISQYSNDVPYPPPLPPAVEAIRKERNITRERFTVLNYKDKFEPGILQLSQWFKEGKLKVKETMAKGLENMGVAFQSMMTGGNVGKQIVCIS 346
                                    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       301       311       321       331       341
   Legend:   → Mismatch (orange background)
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  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 2ZB3)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (PTGR2_MOUSE | Q8VDQ1)
molecular function
    GO:0036132    13-prostaglandin reductase activity    Catalysis of the reaction: 15-keto-prostaglandin + NAD(P)H + H+ -> 13,14-dihydro-15-keto-prostaglandin + NAD(P)+. This reaction is the reduction of 15-keto-prostaglandin.
    GO:0047522    15-oxoprostaglandin 13-oxidase activity    Catalysis of the reaction: (5Z)-(15S)-11-alpha-hydroxy-9,15-dioxoprostanoate + NAD(P)+ -> (5Z)-(15S)-11-alpha-hydroxy-9,15-dioxoprosta-13-enoate + NAD(P)H + H+.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0019371    cyclooxygenase pathway    The chemical reactions and pathways by which prostaglandins are formed from arachidonic acid, and in which prostaglandin-endoperoxide synthase (cyclooxygenase) catalyzes the committed step in the conversion of arachidonic acid to the prostaglandin-endoperoxides PGG2 and PGH2.
    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.
    GO:0006693    prostaglandin metabolic process    The chemical reactions and pathways involving prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring due to the formation of a bond between two carbons of a fatty acid. They have a wide range of biological activities.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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        PTGR2_MOUSE | Q8VDQ1: 1vj1

(-) Related Entries Specified in the PDB File

2zb4 2zb7 2zb8