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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN 15-KETOPROSTAGLANDIN DELTA-13-REDUCTASE IN COMPLEX WITH NADP AND INDOMETHACIN
 
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, Alternative Splicing, Cytoplasm, Nadp, 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: PET32
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PTGR2, ZADH1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    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  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1IMN1Ligand/IonINDOMETHACIN
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1IMN1Ligand/IonINDOMETHACIN
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1IMN2Ligand/IonINDOMETHACIN
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:189 , HIS A:190 , GLU A:191 , ASN A:207 , HOH A:1146 , HOH A:1215BINDING SITE FOR RESIDUE SO4 A 600
2AC2SOFTWAREASP A:211 , ASN A:212 , VAL A:213 , ALA A:214 , HOH A:1061 , HOH A:1136BINDING SITE FOR RESIDUE SO4 A 601
3AC3SOFTWAREPRO 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 , SER A:257 , TYR A:259 , PHE A:287 , LEU A:288 , VAL A:289 , MET A:332 , MET A:333 , GLY A:335 , ASN A:337 , IMN A:800 , HOH A:1016 , HOH A:1019 , HOH A:1038 , HOH A:1039 , HOH A:1042 , HOH A:1043 , HOH A:1044 , HOH A:1045 , HOH A:1110 , HOH A:1224 , HOH A:1388BINDING SITE FOR RESIDUE NAP A 700
4AC4SOFTWARETYR A:51 , CYS A:54 , THR A:60 , TYR A:100 , TYR A:259 , LEU A:288 , LEU A:290 , NAP A:700 , HOH A:1018 , HOH A:1477BINDING SITE FOR RESIDUE IMN A 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZB8)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:265 -Pro A:266

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZB8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZB8)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZB8)

(-) 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:342
 aligned with PTGR2_HUMAN | Q8N8N7 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:346
                                    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       300       310       320       330       340      
          PTGR2_HUMAN     1 MIVQRVVLNSRPGKNGNPVAENFRMEEVYLPDNINEGQVQVRTLYLSVDPYMRCRMNEDTGTDYITPWQLSQVVDGGGIGIIEESKHTNLTKGDFVTSFYWPWQTKVILDGNSLEKVDPQLVDGHLSYFLGAIGMPGLTSLIGIQEKGHITAGSNKTMVVSGAAGACGSVAGQIGHFLGCSRVVGICGTHEKCILLTSELGFDAAINYKKDNVAEQLRESCPAGVDVYFDNVGGNISDTVISQMNENSHIILCGQISQYNKDVPYPPPLSPAIEAIQKERNITRERFLVLNYKDKFEPGILQLSQWFKEGKLKIKETVINGLENMGAAFQSMMTGGNIGKQIVCIS 346
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------2zb8A02 A:133-313 NAD(P)-binding Rossmann-like Domain                                                                                                                                --------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_zinc_N-2zb8A01 A:166-274                                                                                 ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..........hhh.eeeeeee........eeeeeeeeee...hhhhhh....----..........eeeeeeeeee..........eeeeeeee...eeeee.hhhee.hhhhhh.hhhhhhh..hhhhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh....eeee....hhhhhhhhhh...eeeeee..hhhhhhhhhhheeeeeeeee..hhhhh..........hhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhh.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zb8 A   1 MIVQRVVLNSRPGKNGNPVAENFRMEEVYLPDNINEGQVQVRTLYLSVDPYMRCRMNEDT----ITPWQLSQVVDGGGIGIIEESKHTNLTKGDFVTSFYWPWQTKVILDGNSLEKVDPQLVDGHLSYFLGAIGMPGLTSLIGIQEKGHITAGSNKTMVVSGAAGACGSVAGQIGHFLGCSRVVGICGTHEKCILLTSELGFDAAINYKKDNVAEQLRESCPAGVDVYFDNVGGNISDTVISQMNENSHIILCGQISQYNKDVPYPPPLSPAIEAIQKERNITRERFLVLNYKDKFEPGILQLSQWFKEGKLKIKETVINGLENMGAAFQSMMTGGNIGKQIVCIS 346
                                    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       300       310       320       330       340      
                                                                                      60   65
   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 2ZB8)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (PTGR2_HUMAN | Q8N8N7)
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: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: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.

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 Related Entries

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        PTGR2_HUMAN | Q8N8N7: 2vna 2w4q 2w98 2zb4 2zb7

(-) Related Entries Specified in the PDB File

2zb3 2zb4 2zb7