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(-) Description

Title :  CRYSTAL STRUCTURE OF RETINOL DEHYDRATASE IN COMPLEX WITH ALL-TRANS-4-OXORETINOL AND INACTIVE COFACTOR PAP
 
Authors :  S. Pakhomova, J. Buck, M. E. Newcomer
Date :  18 Aug 04  (Deposition) - 08 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sulfotransferase, Dehydratase, Oxoretinol, Retinol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Pakhomova, J. Buck, M. E. Newcomer
The Structures Of The Unique Sulfotransferase Retinol Dehydratase With Product And Inhibitors Provide Insight Into Enzyme Mechanism And Inhibition.
Protein Sci. V. 14 176 2005
PubMed-ID: 15608121  |  Reference-DOI: 10.1110/PS.041061105
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RETINOL DEHYDRATASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-19B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: FALL ARMYWORM
    Organism Scientific: SPODOPTERA FRUGIPERDA
    Organism Taxid: 7108

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1A3P2Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE
2CA2Ligand/IonCALCIUM ION
3HG2Ligand/IonMERCURY (II) ION
4OXR2Ligand/Ion4-OXORETINOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:316 , GLY A:317 , CYS A:318BINDING SITE FOR RESIDUE HG A 1103
2AC2SOFTWAREALA B:316 , GLY B:317 , CYS B:318BINDING SITE FOR RESIDUE HG B 2203
3AC3SOFTWAREGLU A:118 , ASN A:121 , ASP A:122 , HOH A:1243BINDING SITE FOR RESIDUE CA A 1104
4AC4SOFTWAREGLU B:118 , ASN B:121 , ASP B:122BINDING SITE FOR RESIDUE CA B 2204
5AC5SOFTWAREARG A:73 , SER A:74 , GLY A:75 , THR A:76 , THR A:77 , MET A:78 , ARG A:185 , SER A:193 , TYR A:248 , LEU A:282 , PHE A:284 , PHE A:287 , ILE A:311 , ARG A:312 , LYS A:313 , GLY A:314 , HOH B:2205 , HOH B:2219 , HOH B:2221 , HOH B:2337BINDING SITE FOR RESIDUE A3P B 1101
6AC6SOFTWAREARG B:73 , SER B:74 , GLY B:75 , THR B:76 , THR B:77 , MET B:78 , ARG B:185 , SER B:193 , TYR B:248 , LEU B:282 , PHE B:284 , PHE B:287 , ARG B:312 , LYS B:313 , GLY B:314 , HOH B:2208 , HOH B:2209 , HOH B:2235 , HOH B:2264BINDING SITE FOR RESIDUE A3P B 2201
7AC7SOFTWARETYR A:105 , LEU A:138 , LEU A:139 , LYS A:162 , HIS A:164 , HIS A:197 , LEU A:201 , PHE A:310 , HOH B:2337BINDING SITE FOR RESIDUE OXR A 1102
8AC8SOFTWAREPHE B:31 , TYR B:105 , TYR B:120 , LEU B:138 , LEU B:139 , SER B:142 , LYS B:162 , HIS B:164 , HIS B:197 , HOH B:2264BINDING SITE FOR RESIDUE OXR B 2202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X8L)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:225 -Pro A:226
2Thr B:225 -Pro B:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X8L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X8L)

(-) Exons   (0, 0)

(no "Exon" information available for 1X8L)

(-) 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:342
 aligned with Q26490_SPOFR | Q26490 from UniProtKB/TrEMBL  Length:351

    Alignment length:342
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347  
         Q26490_SPOFR     8 PFPYEFRELNPEEDKLVKANLGAFPTTYVKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTTMTQELVWLIENDLNFEAAKTYMSLRYIYLDGFMIYDPEKQEEYNDILPNPENLDMERYLGLLEYFSRPGSSLLAAVPPTEKRFVKTHLPLSLMPPNMLDTVKMVYLARDPRDVAVSSFHHARLLYLLNKQSNFKDFWEMFHRGLYTLTPYFEHVKEAWAKRHDPNMLFLFYEDYLKDLPGCIARIADFLGKKLSEEQIQRLCEHLNFEKFKNNGAVNMEDYREIGILADGEHFIRKGKAGCWRDYFDEEMTKQAEKWIKDNLKDTDLRYPNM 349
               SCOP domains d1x8la_ A: automated matches                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1x8lA00 A:8-349 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....ee..hhhhhhhhhhhhh.....eeee....eeee.hhhhhhhhhhh.......eeeee....hhhhhhhhhhhhhh....hhhhhhhhhhhee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhh......eeee..hhhhh..hhhhh.eeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh......hhhhhhh..............hhhhhh.hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1x8l A   8 PFPYEFRELNPEEDKLVKANLGAFPTTYVKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTTMTQELVWLIENDLNFEAAKTYMSLRYIYLDGFMIYDPEKQEEYNDILPNPENLDMERYLGLLEYSSRPGSSLLAAVPPTEKRFVKTHLPLSLMPPNMLDTVKMVYLARDPRDVAVSSFHHARLLYLLNKQSNFKDFWEMFHRGLYTLTPYFEHVKEAWAKRHDPNMLFLFYEDYLKDLPGSIARIADFLGKKLSEEQIQRLSEHLNFEKFKNNGAVNMEDYREIGILADGEHFIRKGKAGCWRDYFDEEMTKQAEKWIKDNLKDTDLRYPNM 349
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347  


Chain B from PDB  Type:PROTEIN  Length:342
 aligned with Q26490_SPOFR | Q26490 from UniProtKB/TrEMBL  Length:351

    Alignment length:342
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347  
         Q26490_SPOFR     8 PFPYEFRELNPEEDKLVKANLGAFPTTYVKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTTMTQELVWLIENDLNFEAAKTYMSLRYIYLDGFMIYDPEKQEEYNDILPNPENLDMERYLGLLEYFSRPGSSLLAAVPPTEKRFVKTHLPLSLMPPNMLDTVKMVYLARDPRDVAVSSFHHARLLYLLNKQSNFKDFWEMFHRGLYTLTPYFEHVKEAWAKRHDPNMLFLFYEDYLKDLPGCIARIADFLGKKLSEEQIQRLCEHLNFEKFKNNGAVNMEDYREIGILADGEHFIRKGKAGCWRDYFDEEMTKQAEKWIKDNLKDTDLRYPNM 349
               SCOP domains d1x8lb_ B: automated matches                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1x8lB00 B:8-349 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) -------------------------------------------------------Sulfotransfer_1-1x8lB01 B:63-343                                                                                                                                                                                                                                                         ------ Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------Sulfotransfer_1-1x8lB02 B:63-343                                                                                                                                                                                                                                                         ------ Pfam domains (2)
         Sec.struct. author .....ee..hhhhhhhhhhhhh.....eeee....eeee..hhhhhhhhhh.......eeeee....hhhhhhhhhhhhhh....hhhhhhhhhhhee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee..hhhhh..hhhhh.eeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh......hhhhhhh..............hhhhhh.hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1x8l B   8 PFPYEFRELNPEEDKLVKANLGAFPTTYVKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTTMTQELVWLIENDLNFEAAKTYMSLRYIYLDGFMIYDPEKQEEYNDILPNPENLDMERYLGLLEYSSRPGSSLLAAVPPTEKRFVKTHLPLSLMPPNMLDTVKMVYLARDPRDVAVSSFHHARLLYLLNKQSNFKDFWEMFHRGLYTLTPYFEHVKEAWAKRHDPNMLFLFYEDYLKDLPGSIARIADFLGKKLSEEQIQRLSEHLNFEKFKNNGAVNMEDYREIGILADGEHFIRKGKAGCWRDYFDEEMTKQAEKWIKDNLKDTDLRYPNM 349
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q26490_SPOFR | Q26490)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008146    sulfotransferase activity    Catalysis of the transfer of a sulfate group from 3'-phosphoadenosine 5'-phosphosulfate to the hydroxyl group of an acceptor, producing the sulfated derivative and 3'-phosphoadenosine 5'-phosphate.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q26490_SPOFR | Q26490: 1fmj 1fml 1x8j 1x8k

(-) Related Entries Specified in the PDB File

1fml THE SAME PROTEIN COMPLEXED WITH RETINOL
1x8j CRYSTAL STRUCTURE OF RETINOL DEHYDRATASE IN COMPLEX WITH ANDROSTERONE AND INACTIVE COFACTOR PAP
1x8k THE STRUCTURES OF THE UNIQUE SULFOTRANSFERASE RETINOL DEHYDRATASE WITH PRODUCT AND INHIBITORS PROVIDE INSIGHT INTO ENZYME MECHANISM AND INHIBITION.