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(-) Description

Title :  X-RAY STRUCTURE OF THE SUBSTRATE-FREE MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 CYP125, ALTERNATIVE CRYSTAL FORM
 
Authors :  H. Ouellet, P. M. Kells, P. R. Ortiz De Montellano, L. M. Podust
Date :  10 Feb 10  (Deposition) - 10 Nov 10  (Release) - 29 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Cholesterol Degradation, Monooxygenase, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ouellet, P. M. Kells, P. R. Ortiz De Montellano, L. M. Podust
Reverse Type I Inhibitor Of Mycobacteriumtuberculosis Cyp125A1.
Bioorg. Med. Chem. Lett. V. 21 332 2011
PubMed-ID: 21109436  |  Reference-DOI: 10.1016/J.BMCL.2010.11.007

(-) Compounds

Molecule 1 - PUTATIVE CYTOCHROME P450 125
    Chains: A
    EC Number: 1.14.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCWORI
    Expression System Strain: HMS174(DE3)
    Expression System Taxid: 562
    Fragment: RESIDUES 17-433
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: CYP125A1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:116 , LEU A:117 , HIS A:124 , ARG A:128 , MET A:264 , ALA A:268 , GLY A:269 , THR A:272 , THR A:273 , SER A:276 , PRO A:312 , PHE A:316 , ARG A:318 , GLY A:368 , PHE A:369 , GLY A:370 , HIS A:375 , TYR A:376 , CYS A:377 , ILE A:378 , HOH A:2517 , HOH A:2593 , HOH A:2712 , HOH A:2713BINDING SITE FOR RESIDUE HEM A1434

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X5L)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:121 -Pro A:122
2Asn A:362 -Pro A:363

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X5L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X5L)

(-) Exons   (0, 0)

(no "Exon" information available for 2X5L)

(-) 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:414
 aligned with CP125_MYCTO | P9WPP0 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:414
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429    
          CP125_MYCTO    20 PNLPPGFDFTDPAIYAERLPVAEFAELRSAAPIWWNGQDPGKGGGFHDGGFWAITKLNDVKEISRHSDVFSSYENGVIPRFKNDIAREDIEVQRFVMLNMDAPHHTRLRKIISRGFTPRAVGRLHDELQERAQKIAAEAAAAGSGDFVEQVSCELPLQAIAGLLGVPQEDRGKLFHWSNEMTGNEDPEYAHIDPKASSAELIGYAMKMAEEKAKNPADDIVTQLIQADIDGEKLSDDEFGFFVVMLAVAGNETTRNSITQGMMAFAEHPDQWELYKKVRPETAADEIVRWATPVTAFQRTALRDYELSGVQIKKGQRVVMFYRSANFDEEVFQDPFTFNILRNPNPHVGFGGTGAHYCIGANLARMTINLIFNAVADHMPDLKPISAPERLRSGWLNGIKHWQVDYTGRCPVAH 433
               SCOP domains d2x5la_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-2x5lA01 A:300-397                                                                            ------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhh...hhhhhhhhhhhh.eeeee............eeeee.hhhhhhhhhhh...ee..............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...eeeeee...eee..eee....eeeeehhhhh.................................hhhhhhhhhhhhhhhhhhhh...ee....ee........eee.eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2x5l A  20 PNLPPGFDFTDPAIYAERLPVAEFAELRSAAPIWWNGQDPGKGGGFHDGGFWAITKLNDVKEISRHSDVFSSYENGVIPRFKNDIAREDIEVQRFVMLNMDAPHHTRLRKIISRGFTPRAVGRLHDELQERAQKIAAEAAAAGSGDFVEQVSCELPLQAIAGLLGVPQEDRGKLFHWSNEMTGNEDPEYAHIDPKASSAELIGYAMKMAEEKAKNPADDIVTQLIQADIDGEKLSDDEFGFFVVMLAVAGNETTRNSITQGMMAFAEHPDQWELYKKVRPETAADEIVRWATPVTAFQRTALRDYELSGVQIKKGQRVVMFYRSANFDEEVFQDPFTFNILRNPNPHVGFGGTGAHYCIGANLARMTINLIFNAVADHMPDLKPISAPERLRSGWLNGIKHWQVDYTGRLPVAH 433
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429    


Chain A from PDB  Type:PROTEIN  Length:414
 aligned with CP125_MYCTU | P9WPP1 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:414
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429    
          CP125_MYCTU    20 PNLPPGFDFTDPAIYAERLPVAEFAELRSAAPIWWNGQDPGKGGGFHDGGFWAITKLNDVKEISRHSDVFSSYENGVIPRFKNDIAREDIEVQRFVMLNMDAPHHTRLRKIISRGFTPRAVGRLHDELQERAQKIAAEAAAAGSGDFVEQVSCELPLQAIAGLLGVPQEDRGKLFHWSNEMTGNEDPEYAHIDPKASSAELIGYAMKMAEEKAKNPADDIVTQLIQADIDGEKLSDDEFGFFVVMLAVAGNETTRNSITQGMMAFAEHPDQWELYKKVRPETAADEIVRWATPVTAFQRTALRDYELSGVQIKKGQRVVMFYRSANFDEEVFQDPFTFNILRNPNPHVGFGGTGAHYCIGANLARMTINLIFNAVADHMPDLKPISAPERLRSGWLNGIKHWQVDYTGRCPVAH 433
               SCOP domains d2x5la_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-2x5lA01 A:300-397                                                                            ------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhh...hhhhhhhhhhhh.eeeee............eeeee.hhhhhhhhhhh...ee..............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...eeeeee...eee..eee....eeeeehhhhh.................................hhhhhhhhhhhhhhhhhhhh...ee....ee........eee.eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2x5l A  20 PNLPPGFDFTDPAIYAERLPVAEFAELRSAAPIWWNGQDPGKGGGFHDGGFWAITKLNDVKEISRHSDVFSSYENGVIPRFKNDIAREDIEVQRFVMLNMDAPHHTRLRKIISRGFTPRAVGRLHDELQERAQKIAAEAAAAGSGDFVEQVSCELPLQAIAGLLGVPQEDRGKLFHWSNEMTGNEDPEYAHIDPKASSAELIGYAMKMAEEKAKNPADDIVTQLIQADIDGEKLSDDEFGFFVVMLAVAGNETTRNSITQGMMAFAEHPDQWELYKKVRPETAADEIVRWATPVTAFQRTALRDYELSGVQIKKGQRVVMFYRSANFDEEVFQDPFTFNILRNPNPHVGFGGTGAHYCIGANLARMTINLIFNAVADHMPDLKPISAPERLRSGWLNGIKHWQVDYTGRLPVAH 433
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429
   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, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X5L)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: p450] (161)

(-) Gene Ontology  (12, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CP125_MYCTU | P9WPP1)
molecular function
    GO:0036199    cholest-4-en-3-one 26-monooxygenase activity    Catalysis of the reaction: cholest-4-en-3-one + NADH + H+ + O2 = 26-hydroxycholest-4-en-3-one + NAD+ + H2O. This reaction involves the hydroxylation of the C26 carbon, followed by oxidation of the alcohol to the carboxylic acid via the aldehyde intermediate.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    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:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
    GO:0008395    steroid hydroxylase activity    Catalysis of the formation of a hydroxyl group on a steroid by incorporation of oxygen from O2.
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:0044117    growth of symbiont in host    The increase in size or mass of an organism, occurring within the cells or tissues of the host organism. This may (but not necessarily) include a filamentous growth form, and also can include secretion of proteases and lipases to break down host tissue. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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.
cellular component
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A   (CP125_MYCTO | P9WPP0)
molecular function
    GO:0036199    cholest-4-en-3-one 26-monooxygenase activity    Catalysis of the reaction: cholest-4-en-3-one + NADH + H+ + O2 = 26-hydroxycholest-4-en-3-one + NAD+ + H2O. This reaction involves the hydroxylation of the C26 carbon, followed by oxidation of the alcohol to the carboxylic acid via the aldehyde intermediate.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    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:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
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

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

UniProtKB/Swiss-Prot
        CP125_MYCTO | P9WPP0: 2x5w 2xc3 2xn8 3ivy 3iw0 3iw1 3iw2
        CP125_MYCTU | P9WPP1: 2x5w 2xc3 2xn8 3ivy 3iw0 3iw1 3iw2

(-) Related Entries Specified in the PDB File

2x5w X-RAY STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 CYP125 IN COMPLEX WITH SUBSTRATE CHOLEST-4-EN-3-ONE
2xc3 X-RAY STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYP125 BOUND TO THE REVERSE TYPE I INHIBITOR
2xn8 X-RAY STRUCTURE OF THE SUBSTRATE-FREE MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 CYP125