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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ZINC-BINDING ALCOHOL DEHYDROGENASE 1 (ZADH1) IN TERNARY COMPLEX WITH NADP AND 18BETA-GLYCYRRHETINIC ACID
 
Authors :  N. Shafqat, W. W. Yue, E. Ugochukwu, S. Picaud, F. Niesen, C. Arrowsmith J. Weigelt, A. Edwards, C. Bountra, U. Oppermann
Date :  30 Nov 08  (Deposition) - 20 Jan 09  (Release) - 04 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  15-Oxoprostalglandin, Medium-Chain Dehydrogenase/Reductase, Nadp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Shafqat, W. W. Yue, F. Niesen, U. Oppermann
Crystal Structure Of Human Zinc-Binding Alcohol Dehydrogenase 1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROSTAGLANDIN REDUCTASE 2
    Chains: A
    EC Number: 1.3.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-CTHF
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: R3-PRARE2
    Expression System Vector: PET-BASED VECTOR
    Fragment: CATALYTIC DOMAIN, RESIDUES 1-349
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 15-OXOPROSTAGLANDIN 13-REDUCTASE, ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 1, PRG-2, ZINC-BINDING ALCOHOL DEHYDROGENASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1CBW2Ligand/Ion(3BETA,5BETA,14BETA)-3-HYDROXY-11-OXOOLEAN-12-EN-29-OIC ACID
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
3SO44Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:50 , 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 , CYS A:253 , GLY A:254 , ILE A:256 , SER A:257 , TYR A:259 , PHE A:287 , VAL A:289 , MET A:332 , MET A:333 , GLY A:335 , ASN A:337 , GLY A:339 , CBW A:1350 , HOH A:2085 , HOH A:2171 , HOH A:2172 , HOH A:2173 , HOH A:2174 , HOH A:2175 , HOH A:2176 , HOH A:2177 , HOH A:2178 , HOH A:2179 , HOH A:2181 , HOH A:2182BINDING SITE FOR RESIDUE NAP A1349
2AC2SOFTWARETYR A:51 , TYR A:64 , PHE A:99 , TYR A:100 , CYS A:253 , GLY A:254 , GLN A:255 , TYR A:259 , TYR A:265 , NAP A:1349 , HOH A:2058 , HOH A:2183BINDING SITE FOR RESIDUE CBW A1350
3AC3SOFTWAREARG A:24 , GLU A:26 , LYS A:116 , VAL A:117 , PHE A:129 , GLU A:297 , HOH A:2073 , HOH A:2184BINDING SITE FOR RESIDUE CBW A1351
4AC4SOFTWAREASP A:211 , ASN A:212 , VAL A:213 , ALA A:214 , HOH A:2116 , HOH A:2185 , HOH A:2186BINDING SITE FOR RESIDUE SO4 A1352
5AC5SOFTWARETHR A:189 , HIS A:190 , GLU A:191 , HOH A:2187BINDING SITE FOR RESIDUE SO4 A1353
6AC6SOFTWAREGLU A:285 , ARG A:286BINDING SITE FOR RESIDUE SO4 A1354
7AC7SOFTWAREALA A:214 , ARG A:218BINDING SITE FOR RESIDUE SO4 A1355

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W4Q)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W4Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W4Q)

(-) Exons   (0, 0)

(no "Exon" information available for 2W4Q)

(-) 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:349
 aligned with PTGR2_HUMAN | Q8N8N7 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:349
                             1                                                                                                                                                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339         
          PTGR2_HUMAN     - -MIVQRVVLNSRPGKNGNPVAENFRMEEVYLPDNINEGQVQVRTLYLSVDPYMRCRMNEDTGTDYITPWQLSQVVDGGGIGIIEESKHTNLTKGDFVTSFYWPWQTKVILDGNSLEKVDPQLVDGHLSYFLGAIGMPGLTSLIGIQEKGHITAGSNKTMVVSGAAGACGSVAGQIGHFLGCSRVVGICGTHEKCILLTSELGFDAAINYKKDNVAEQLRESCPAGVDVYFDNVGGNISDTVISQMNENSHIILCGQISQYNKDVPYPPPLSPAIEAIQKERNITRERFLVLNYKDKFEPGILQLSQWFKEGKLKIKETVINGLENMGAAFQSMMTGGNIGKQIVCISEE 348
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------2w4qA02 A:133-313 NAD(P)-binding Rossmann-like Domain                                                                                                                                ----------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_zinc_N-2w4qA01 A:166-274                                                                                 -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..........hhh.eeeeeeee.......eeeeeeeeee...hhhhhh..................eeeeeeeeeee.........eeeeeeee...eeeee.hhhee.hhhhhh.hhhhhhh..hhhhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh....eeee....hhhhhhhhhh...eeeeee..hhhhhhhhhh.eeeeeeeee..hhhhh..........hhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhh.....eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w4q A   0 MMIVQRVVLNSRPGKNGNPVAENFRMEEVYLPDNINEGQVQVRTLYLSVDPYMRCRMNEDTGTDYITPWQLSQVVDGGGIGIIEESKHTNLTKGDFVTSFYWPWQTKVILDGNSLEKVDPQLVDGHLSYFLGAIGMPGLTSLIGIQEKGHITAGSNKTMVVSGAAGACGSVAGQIGHFLGCSRVVGICGTHEKCILLTSELGFDAAINYKKDNVAEQLRESCPAGVDVYFDNVGGNISDTVISQMNENSHIILCGQISQYNKDVPYPPPLSPAIEAIQKERNITRERFLVLNYKDKFEPGILQLSQWFKEGKLKIKETVINGLENMGAAFQSMMTGGNIGKQIVCISEE 348
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339
   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 2W4Q)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological 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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        PTGR2_HUMAN | Q8N8N7: 2vna 2w98 2zb4 2zb7 2zb8

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