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(-) Description

Title :  CRYSTAL STRUCTURE OF RETINOL DEHYDRATASE IN A COMPLEX WITH RETINOL AND PAP
 
Authors :  S. Pakhomova, M. Kobayashi, J. Buck, M. E. Newcomer
Date :  17 Aug 00  (Deposition) - 02 May 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Sulfotransferase, Dehydratase, Retinol, Adenosine 3', 5'- Diphosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Pakhomova, M. Kobayashi, J. Buck, M. E. Newcomer
A Helical Lid Converts A Sulfotransferase To A Dehydratase.
Nat. Struct. Biol. V. 8 447 2001
PubMed-ID: 11323722  |  Reference-DOI: 10.1038/87617
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RETINOL DEHYDRATASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: FALL ARMYWORM
    Organism Scientific: SPODOPTERA FRUGIPERDA
    Organism Taxid: 7108

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1A3P2Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE
2CA2Ligand/IonCALCIUM ION
3RTL2Ligand/IonRETINOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1A3P1Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3RTL1Ligand/IonRETINOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1A3P1Ligand/IonADENOSINE-3'-5'-DIPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3RTL1Ligand/IonRETINOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:121 , ASP A:122BINDING SITE FOR RESIDUE CA A 450
2AC2SOFTWAREGLU B:118 , ASN B:121 , ASP B:122BINDING SITE FOR RESIDUE CA B 550
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 , ARG A:312 , LYS A:313 , GLY A:314 , HOH A:467 , HOH A:494BINDING SITE FOR RESIDUE A3P A 400
4AC4SOFTWARETYR A:105 , LEU A:139 , SER A:142 , LYS A:162 , HIS A:164 , HIS A:197 , TYR A:298 , PHE A:310 , HOH A:467BINDING SITE FOR RESIDUE RTL A 401
5AC5SOFTWAREARG 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:560BINDING SITE FOR RESIDUE A3P B 500
6AC6SOFTWARETYR B:105 , ILE B:111 , LEU B:138 , LEU B:139 , SER B:142 , LYS B:162 , HIS B:164 , HIS B:197 , LEU B:201 , TYR B:298 , HOH B:560BINDING SITE FOR RESIDUE RTL B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric 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 1FML)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1FML)

(-) 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:341
 aligned with Q26490_SPOFR | Q26490 from UniProtKB/TrEMBL  Length:351

    Alignment length:341
                                    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 LPFPYEFRELNPEEDKLVKANLGAFPTTYVKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTTMTQELVWLIENDLNFEAAKTYMSLRYIYLDGFMIYDPEKQEEYNDILPNPENLDMERYLGLLEYFSRPGSSLLAAVPPTEKRFVKTHLPLSLMPPNMLDTVKMVYLARDPRDVAVSSFHHARLLYLLNKQSNFKDFWEMFHRGLYTLTPYFEHVKEAWAKRHDPNMLFLFYEDYLKDLPGCIARIADFLGKKLSEEQIQRLCEHLNFEKFKNNGAVNMEDYREIGILADGEHFIRKGKAGCWRDYFDEEMTKQAEKWIKDNLKDTDLRYP 347
               SCOP domains d1fmla_ A: Retinol dehydratase                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1fmlA00 A:7-347 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee..hhhhhhhhhhhhh.....eeee....eeee..hhhhhhhhhh.......eeeee....hhhhhhhhhhhhhh....hhhhhhhhhhhee.......hhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhh.......eeee..hhhhh..hhhhh.eeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......hhhhhhh..............hhhhhh.hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fml A   7 LPFPYEFRELNPEEDKLVKANLGAFPTTYVKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTTMTQELVWLIENDLNFEAAKTYMSLRYIYLDGFMIYDPEKQEEYNDILPNPENLDMERYLGLLEYSSRPGSSLLAAVPPTEKRFVKTHLPLSLMPPNMLDTVKMVYLARDPRDVAVSSFHHARLLYLLNKQSNFKDFWEMFHRGLYTLTPYFEHVKEAWAKRHDPNMLFLFYEDYLKDLPGCIARIADFLGKKLSEEQIQRLCEHLNFEKFKNNGAVNMEDYREIGILADGEHFIRKGKAGCWRDYFDEEMTKQAEKWIKDNLKDTDLRYP 347
                                    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:341
 aligned with Q26490_SPOFR | Q26490 from UniProtKB/TrEMBL  Length:351

    Alignment length:341
                                    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 LPFPYEFRELNPEEDKLVKANLGAFPTTYVKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTTMTQELVWLIENDLNFEAAKTYMSLRYIYLDGFMIYDPEKQEEYNDILPNPENLDMERYLGLLEYFSRPGSSLLAAVPPTEKRFVKTHLPLSLMPPNMLDTVKMVYLARDPRDVAVSSFHHARLLYLLNKQSNFKDFWEMFHRGLYTLTPYFEHVKEAWAKRHDPNMLFLFYEDYLKDLPGCIARIADFLGKKLSEEQIQRLCEHLNFEKFKNNGAVNMEDYREIGILADGEHFIRKGKAGCWRDYFDEEMTKQAEKWIKDNLKDTDLRYP 347
               SCOP domains d1fmlb_ B: Retinol dehydratase                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1fmlB00 B:7-347 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee..hhhhhhhhhhhhh.....eeee....eeee..hhhhhhhhhh.......eeeee....hhhhhhhhhhhhhh....hhhhhhhhhhhee.......hhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhh.......eeee..hhhhh..hhhhh.eeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhh..............hhhhhh.hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fml B   7 LPFPYEFRELNPEEDKLVKANLGAFPTTYVKLGPKGYMVYRPYLKDAANIYNMPLRPTDVFVASYQRSGTTMTQELVWLIENDLNFEAAKTYMSLRYIYLDGFMIYDPEKQEEYNDILPNPENLDMERYLGLLEYSSRPGSSLLAAVPPTEKRFVKTHLPLSLMPPNMLDTVKMVYLARDPRDVAVSSFHHARLLYLLNKQSNFKDFWEMFHRGLYTLTPYFEHVKEAWAKRHDPNMLFLFYEDYLKDLPGCIARIADFLGKKLSEEQIQRLCEHLNFEKFKNNGAVNMEDYREIGILADGEHFIRKGKAGCWRDYFDEEMTKQAEKWIKDNLKDTDLRYP 347
                                    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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FML)

(-) Gene Ontology  (2, 2)

Asymmetric 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 1x8j 1x8k 1x8l

(-) Related Entries Specified in the PDB File

1fmj 1FMJ IS THE MERCURY DERIVATIVE OF THE SAME PROTEIN.