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(-) Description

Title :  CRYSTAL STRUCTURE OF RETINOL DEHYDRATASE IN COMPLEX WITH ANDROSTERONE AND INACTIVE COFACTOR PAP
 
Authors :  S. Pakhomova, J. Buck, M. E. Newcomer
Date :  18 Aug 04  (Deposition) - 08 Feb 05  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sulfotransferase, Dehydratase, Steroid Binding. , Transferase (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 Int Enzyme Mechanism And Inhibition.
Protein Sci. V. 14 176 2005
PubMed-ID: 15608121  |  Reference-DOI: 10.1110/PS.041061105

(-) 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  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1A3P2Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE
2AOI2Ligand/IonANDROSTERONE
3CA2Ligand/IonCALCIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:118 , ASN A:121 , ASP A:122BINDING SITE FOR RESIDUE CA A 600
2AC2SOFTWAREGLU B:118 , ASN B:121 , ASP B:122BINDING SITE FOR RESIDUE CA B 700
3AC3SOFTWAREARG 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 A:635 , HOH A:646 , HOH A:650BINDING SITE FOR RESIDUE A3P A 601
4AC4SOFTWAREHOH A:606 , HOH A:653 , ARG 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 , ILE B:311 , ARG B:312 , LYS B:313 , GLY B:314 , HOH B:732BINDING SITE FOR RESIDUE A3P A 602
5AC5SOFTWAREPHE A:31 , GLY A:108 , ILE A:111 , LEU A:201 , TYR A:298 , HOH A:629 , HOH A:637BINDING SITE FOR RESIDUE AOI A 400
6AC6SOFTWAREPHE B:31 , GLY B:108 , ILE B:111 , TYR B:298 , HOH B:727 , HOH B:735BINDING SITE FOR RESIDUE AOI B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X8J)

(-) 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 1X8J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X8J)

(-) Exons   (0, 0)

(no "Exon" information available for 1X8J)

(-) 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:343
 aligned with Q26490_SPOFR | Q26490 from UniProtKB/TrEMBL  Length:351

    Alignment length:343
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346   
         Q26490_SPOFR     7 LPFPYEFRELNPEEDKLVKANLGAFPTTYVKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTTMTQELVWLIENDLNFEAAKTYMSLRYIYLDGFMIYDPEKQEEYNDILPNPENLDMERYLGLLEYFSRPGSSLLAAVPPTEKRFVKTHLPLSLMPPNMLDTVKMVYLARDPRDVAVSSFHHARLLYLLNKQSNFKDFWEMFHRGLYTLTPYFEHVKEAWAKRHDPNMLFLFYEDYLKDLPGCIARIADFLGKKLSEEQIQRLCEHLNFEKFKNNGAVNMEDYREIGILADGEHFIRKGKAGCWRDYFDEEMTKQAEKWIKDNLKDTDLRYPNM 349
               SCOP domains d1x8ja_ A: automated matches                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1x8jA00 A:7-349 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee..hhhhhhhhhhhhh.....eeee....eeee..hhhhhhhhhh.......eeeee....hhhhhhhhhhhhhh....hhhhhhhhhhhee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhh......eeee..hhhhh..hhhhh.eeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh......hhhhhhh..............hhhhhh.hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x8j A   7 LPFPYEFRELNPEEDKLVKANLGAFPTTYVKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTTMTQELVWLIENDLNFEAAKTYMSLRYIYLDGFMIYDPEKQEEYNDILPNPENLDMERYLGLLEYSSRPGSSLLAAVPPTEKRFVKTHLPLSLMPPNMLDTVKMVYLARDPRDVAVSSFHHARLLYLLNKQSNFKDFWEMFHRGLYTLTPYFEHVKEAWAKRHDPNMLFLFYEDYLKDLPGSIARIADFLGKKLSEEQIQRLSEHLNFEKFKNNGAVNMEDYREIGILADGEHFIRKGKAGCWRDYFDEEMTKQAEKWIKDNLKDTDLRYPNM 349
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346   


Chain B from PDB  Type:PROTEIN  Length:343
 aligned with Q26490_SPOFR | Q26490 from UniProtKB/TrEMBL  Length:351

    Alignment length:343
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346   
         Q26490_SPOFR     7 LPFPYEFRELNPEEDKLVKANLGAFPTTYVKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTTMTQELVWLIENDLNFEAAKTYMSLRYIYLDGFMIYDPEKQEEYNDILPNPENLDMERYLGLLEYFSRPGSSLLAAVPPTEKRFVKTHLPLSLMPPNMLDTVKMVYLARDPRDVAVSSFHHARLLYLLNKQSNFKDFWEMFHRGLYTLTPYFEHVKEAWAKRHDPNMLFLFYEDYLKDLPGCIARIADFLGKKLSEEQIQRLCEHLNFEKFKNNGAVNMEDYREIGILADGEHFIRKGKAGCWRDYFDEEMTKQAEKWIKDNLKDTDLRYPNM 349
               SCOP domains d1x8jb_ B: automated matches                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1x8jB00 B:7-349 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                                    CATH domains
           Pfam domains (1) --------------------------------------------------------Sulfotransfer_1-1x8jB01 B:63-343                                                                                                                                                                                                                                                         ------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------Sulfotransfer_1-1x8jB02 B:63-343                                                                                                                                                                                                                                                         ------ Pfam domains (2)
         Sec.struct. author ......ee..hhhhhhhhhhhhh.....eeee....eeee..hhhhhhhhhh.......eeeee....hhhhhhhhhhhhhh....hhhhhhhhhhhee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhh......eeee..hhhhh..hhhhh.eeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh......hhhhhhh..............hhhhhh.hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x8j B   7 LPFPYEFRELNPEEDKLVKANLGAFPTTYVKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTTMTQELVWLIENDLNFEAAKTYMSLRYIYLDGFMIYDPEKQEEYNDILPNPENLDMERYLGLLEYSSRPGSSLLAAVPPTEKRFVKTHLPLSLMPPNMLDTVKMVYLARDPRDVAVSSFHHARLLYLLNKQSNFKDFWEMFHRGLYTLTPYFEHVKEAWAKRHDPNMLFLFYEDYLKDLPGSIARIADFLGKKLSEEQIQRLSEHLNFEKFKNNGAVNMEDYREIGILADGEHFIRKGKAGCWRDYFDEEMTKQAEKWIKDNLKDTDLRYPNM 349
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346
   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 1x8k 1x8l

(-) Related Entries Specified in the PDB File

1fml THE SAME PROTEIN COMPLEXED WITH RETINOL
1x8k CRYSTAL STRUCTURE OF RETINOL DEHYDRATASE IN COMPLEX WITH ANHYDRORETINOL AND INACTIVE COFACTOR PAP
1x8l CRYSTAL STRUCTURE OF RETINOL DEHYDRATASE IN COMPLEX WITH ALL-TRANS-4-OXORETINOL AND INACTIVE COFACTOR PAP