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(-) Description

Title :  THE CRYSTAL STRUCTURE OF 3-KETOSTEROID-DELTA4-(5ALPHA)-DEHYDROGENASE FROM RHODOCOCCUS JOSTII RHA1
 
Authors :  N. Van Oosterwijk, J. Knol, L. Dijkhuizen, R. Van Der Geize, B. W. Dij
Date :  03 May 12  (Deposition) - 01 Aug 12  (Release) - 10 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase, Dehydogenase, Steroid Catabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Van Oosterwijk, J. Knol, L. Dijkhuizen, R. Van Der Geize, B. W. Dijkstra
Structure And Catalytic Mechanism Of 3-Ketosteroid-{Delta}4 (5Alpha)-Dehydrogenase From Rhodococcus Jostii Rha1 Genome.
J. Biol. Chem. V. 287 30975 2012
PubMed-ID: 22833669  |  Reference-DOI: 10.1074/JBC.M112.374306

(-) Compounds

Molecule 1 - 3-KETOSTEROID-DELTA4-5ALPHA-DEHYDROGENASE
    Chains: A
    EC Number: 1.3.99.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: RHODOCOCCUS JOSTII
    Organism Taxid: 101510
    Strain: RHA1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4GOL1Ligand/IonGLYCEROL
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4GOL2Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:466 , SER A:468 , GLY A:469 , ACT A:1491 , FAD A:1493 , HOH A:2447BINDING SITE FOR RESIDUE ACT A1490
2AC2SOFTWAREGLY A:64 , GLU A:137 , ACT A:1490 , FAD A:1493 , HOH A:2447 , HOH A:2605BINDING SITE FOR RESIDUE ACT A1491
3AC3SOFTWAREALA A:95 , GLY A:97 , ARG A:322 , HOH A:2164 , HOH A:2451 , HOH A:2606BINDING SITE FOR RESIDUE GOL A1492
4AC4SOFTWAREGLY A:28 , GLY A:30 , ILE A:31 , ALA A:32 , LEU A:50 , GLU A:51 , ARG A:52 , THR A:53 , GLY A:58 , ALA A:59 , THR A:60 , ALA A:63 , GLY A:64 , GLY A:65 , PHE A:66 , MET A:203 , VAL A:205 , ALA A:239 , THR A:240 , GLY A:241 , GLY A:262 , ILE A:265 , GLU A:267 , HIS A:268 , PHE A:427 , GLY A:455 , ARG A:456 , TYR A:466 , GLY A:469 , THR A:470 , SER A:471 , LEU A:472 , ACT A:1490 , ACT A:1491 , HOH A:2039 , HOH A:2086 , HOH A:2094 , HOH A:2110 , HOH A:2363 , HOH A:2593 , HOH A:2608BINDING SITE FOR RESIDUE FAD A1493
5AC5SOFTWAREALA A:263 , ALA A:264 , HOH A:2608BINDING SITE FOR RESIDUE CL A1494

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AT0)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:97 -Pro A:98
2Ala A:153 -Pro A:154
3Thr A:413 -Pro A:414

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AT0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AT0)

(-) Exons   (0, 0)

(no "Exon" information available for 4AT0)

(-) 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:483
 aligned with Q0S4Q9_RHOJR | Q0S4Q9 from UniProtKB/TrEMBL  Length:490

    Alignment length:483
                                    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       356       366       376       386       396       406       416       426       436       446       456       466       476       486   
         Q0S4Q9_RHOJR     7 IRPRSATTVTEWDYEADVVVAGYGIAGVAASIEAARAGADVLVLERTSGWGGAAALAGGFIYLGGGTPLQKACGFDDSPENMKTFMMAALGPGADEEKITDYCEGSVEHYNWLVDCGVPFKESFWGEPGWEPPFDDGLMYSGGENAAPFNEIATPAPRGHVPQMDGKRTGEKGGGYMLMKPLVETAEKLGVRAEYDMRVQTLVTDDTGRVVGIVAKQYGKEVAVRARRGVVLATGSFAYNDKMIEAHAPRLIGRPGAAIEEHDGRSILMAQALGADLAHMDATEVAFVCDPQLIVRGILVNGRGQRYVPEDTYSGRIGQMTLFHQDNQAFLIIDEASYEEGAAATTATPFLRVQPKWAAETVEELESDMGLPAGALQSTVEVYNKHAAEGSDPLLHKKSEWVKPIGTPVAALDLRGFTLGFTLGGLRTTVNSEVLHVSGEPIPGLFAAGRCTSGVCAGGYASGTSLGDGSFYGRRAGISAAKQ 489
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhh....eeeeeeee..hhhhhhhhhhhhhh...eeee........hhhhh...ee....hhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.....................ee........hhhhh......ee..............hhhhhhhhhhhhhhh..eee..eeeeeeee.....eeeeeeee..eeeeeeeeeeeee.......hhhhhhhhhhhhh...........hhhhhhhhh....ee....eeeee..hhhhhh..eee............hhhhhhhhhhhhh....eeeeehhhhhhhhhh...hhhhh....eee.hhhhhhhhh....hhhhhhhhhhhhhhh.........hhhhh......eeeee....eeeee..ee......eee.....eeeeeee.hhh...........hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4at0 A   7 IRPRSATTVTEWDYEADVVVAGYGIAGVAASIEAARAGADVLVLERTSGWGGATALAGGFIYLGGGTPLQKACGFDDSPENMKTFMMAALGPGADEEKITDYCEGSVEHYNWLVDCGVPFKESFWGEPGWEPPFDDGLMYSGGENAAPFNEIAAPAPRGHVPQMDGKRTGEKGGGYMLMKPLVETAEKLGVRAEYDMRVQTLVTDDTGRVVGIVAKQYGKEVAVRARRGVVLATGSFAYNDKMIEAHAPRLIGRPGAAIEEHDGRSILMAQALGADLAHMDATEVAFVCDPQLIVRGILVNGRGQRYVPEDTYSGRIGQMTLFHQDNQAFLIIDEASYEEGAAATTATPFLRVQPKWAAETVEELESDMGLPAGALQSTVEVYNKHAAEGSDPLLHKKSEWVKPIGTPVAALDLRGFTLGFTLGGLRTTVNSEVLHVSGEPIPGLFAAGRCTSGVCAGGYASGTSLGDGSFYGRRAGISAAKQ 489
                                    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       356       366       376       386       396       406       416       426       436       446       456       466       476       486
   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 4AT0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AT0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AT0)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q0S4Q9_RHOJR | Q0S4Q9)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.
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.

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 Related Entries

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        Q0S4Q9_RHOJR | Q0S4Q9: 4at2

(-) Related Entries Specified in the PDB File

4at2 THE CRYSTAL STRUCTURE OF 3-KETOSTEROID-DELTA4-(5ALPHA)- DEHYDROGENASE FROM RHODOCOCCUS JOSTII RHA1 IN COMPLEX WITH 4-ANDROSTENE-3,17- DIONE