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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-KETOSTEROID-9-ALPHA-HYDROXYLASE (KSHA) FROM M. TUBERCULOSIS
 
Authors :  I. D'Angelo, J. Capyk, N. Strynadka, L. Eltis
Date :  27 Jan 09  (Deposition) - 03 Mar 09  (Release) - 02 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Ksha, Cholesterol, Rieske, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. K. Capyk, I. D'Angelo, N. C. Strynadka, L. D. Eltis
Characterization Of 3-Ketosteroid 9{Alpha}-Hydroxylase, A Rieske Oxygenase In The Cholesterol Degradation Pathway Of Mycobacterium Tuberculosis
J. Biol. Chem. V. 284 9937 2009
PubMed-ID: 19234303  |  Reference-DOI: 10.1074/JBC.M900719200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POSSIBLE OXIDOREDUCTASE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System VectorPETKA1
    Expression System Vector TypePLASMID
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    StrainH37RV

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1FE21Ligand/IonFE (II) ION
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1FE23Ligand/IonFE (II) ION
2FES3Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:67 , HIS A:69 , MET A:70 , GLY A:72 , CYS A:86 , PHE A:88 , HIS A:89 , TRP A:91BINDING SITE FOR RESIDUE FES A 451
2AC2SOFTWAREHIS A:181 , HIS A:186 , ASP A:304 , HOH A:561BINDING SITE FOR RESIDUE FE2 A 452
3AC3SOFTWARETHR A:177 , ASP A:178 , MET A:179 , GLU A:322 , ASP A:323 , HOH A:435BINDING SITE FOR RESIDUE NA A 387

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:218 -Thr A:219
2Lys A:279 -Gly A:280
3Gly A:280 -Met A:281

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIESKEPS51296 Rieske [2Fe-2S] iron-sulfur domain profile.KSHA_MYCTU26-128  1A:26-128
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIESKEPS51296 Rieske [2Fe-2S] iron-sulfur domain profile.KSHA_MYCTU26-128  3A:26-128

(-) Exons   (0, 0)

(no "Exon" information available for 2ZYL)

(-) 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:359
 aligned with KSHA_MYCTU | P71875 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:361
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373 
           KSHA_MYCTU    14 DAGALPTRYARGWHCLGVAKDYLEGKPHGVEAFGTKLVVFADSHGDLKVLDGYCRHMGGDLSEGTVKGDEVACPFHDWRWGGDGRCKLVPYARRTPRMARTRSWTTDVRSGLLFVWHDHEGNPPDPAVRIPEIPEAASDEWTDWRWNRILIEGSNCRDIIDNVTDMAHFFYIHFGLPTYFKNVFEGHIASQYLHNVGRPDVDDLGTSYGEAHLDSEASYFGPSFMINWLHNRYGNYKSESILINCHYPVTQNSFVLQWGVIVEKPKGMSEEMTDKLSRVFTEGVSKGFLQDVEIWKHKTRIDNPLLVEEDGAVYQLRRWYEQFYVDVADIKPEMVERFEIEVDTKRANEFWNAEVEKNLKS 374
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------Rieske-2zylA01 A:25-118                                                                       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeee.hhhh....eeeee..eeeeeee.....eeeee........hhhhheee..eee......eee....eee..............ee.eeee..eeeeee.......hhhhh...hhhhhh......eeeeeeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeee.............eeeeeeeeee...eeeeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeee.......--.hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------RIESKE  PDB: A:26-128 UniProt: 26-128                                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zyl A  14 DAGALPTRYARGWHCLGVAKDYLEGKPHGVEAFGTKLVVFADSHGDLKVLDGYCRHMGGDLSEGTVKGDEVACPFHDWRWGGDGRCKLVPYARRTPRMARTRSWTTDVRSGLLFVWHDHEGNPPDPAVRIPEIPEAASDEWTDWRWNRILIEGSNCRDIIDNVTDMAHFFYIHFGLPTYFKNVFEGHIASQYLHNVGRPDVDDLGTSYGEAHLDSEASYFGPSFMINWLHNRYGNYKSESILINCHYPVTQNSFVLQWGVIVEKPKGMS--MTDKLSRVFTEGVSKGFLQDVEIWKHKTRIDNPLLVEEDGAVYQLRRWYEQFYVDVADIKPEMVERFEIEVDTKRANEFWNAEVEKNLKS 374
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273        |- |     293       303       313       323       333       343       353       363       373 
                                                                                                                                                                                                                                                                                                      282  |                                                                                         
                                                                                                                                                                                                                                                                                                         285                                                                                         

   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 2ZYL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZYL)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A   (KSHA_MYCTU | P71875)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0036200    3-ketosteroid 9-alpha-monooxygenase activity    Catalysis of the reaction: androsta-1,4-diene-3,17-dione + NADH + H+ + O2 = 9alpha-hydroxyandrosta-1,4-diene-3,17-dione + NAD+ + H2O.
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0047086    ketosteroid monooxygenase activity    Catalysis of the reaction: O2 + NADPH + progesterone = H2O + NADP+ + testosterone acetate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0050292    steroid 9-alpha-monooxygenase activity    Catalysis of the reaction: AH(2) + O(2) + pregna-4,9(11)-diene-3,20-dione = 9,11alpha-epoxypregn-4-ene-3,20-dione + A + H(2)O.
biological process
    GO:0006707    cholesterol catabolic process    The chemical reactions and pathways resulting in the breakdown of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    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:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0070207    protein homotrimerization    The formation of a protein homotrimer, a macromolecular structure consisting of three noncovalently associated identical subunits.
    GO:0070723    response to cholesterol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cholesterol stimulus.
    GO:0006694    steroid biosynthetic process    The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KSHA_MYCTU | P718754qck

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