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(-) Description

Title :  X-RAY STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 CYP125 IN COMPLEX WITH SUBSTRATE CHOLEST-4-EN-3-ONE
 
Authors :  H. Ouellet, S. Guan, J. B. Johnston, E. D. Chow, P. M. Kells, A. L. Burling J. S. Cox, L. M. Podust, P. R. Ortiz De Montellano
Date :  10 Feb 10  (Deposition) - 16 Jun 10  (Release) - 04 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym./Biol. Unit :  A
Keywords :  Cholesterol Degradation, Metal-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ouellet, S. Guan, J. B. Johnston, E. D. Chow, P. M. Kells, A. L. Burlingame, J. S. Cox, L. M. Podust, P. R. O. De Montellano
Mycobacterium Tuberculosis Cyp125A1, A Steroid C27 Monooxygenase That Detoxifies Intracellularly Generated Cholest-4-En-3-One.
Mol. Microbiol. V. 77 730 2010
PubMed-ID: 20545858  |  Reference-DOI: 10.1111/J.1365-2958.2010.07243.X

(-) 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
    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  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3K2B1Ligand/Ion(8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE
4SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:84 , HIS A:85 , HIS A:195 , ASN A:198 , TYR A:208 , HOH A:2226 , HOH A:2239 , HOH A:2432BINDING SITE FOR RESIDUE SO4 A1428
2AC2SOFTWAREASP A:108 , GLN A:112 , MET A:200 , PRO A:213 , LYS A:214 , VAL A:267 , ALA A:268 , TRP A:414 , HEM A:1431 , HOH A:2434BINDING SITE FOR RESIDUE K2B A1429
3AC3SOFTWAREHIS A:210 , TYR A:376 , ALA A:380 , ASN A:381 , ARG A:384 , HOH A:2388BINDING SITE FOR RESIDUE EDO A1430
4AC4SOFTWAREMET A:116 , LEU A:117 , HIS A:124 , ARG A:128 , ILE A:179 , MET A:264 , ALA A:268 , THR A:272 , THR A:273 , PRO A:312 , PHE A:316 , ARG A:318 , GLY A:368 , PHE A:369 , GLY A:370 , HIS A:375 , CYS A:377 , ILE A:378 , GLY A:379 , ALA A:383 , K2B A:1429 , HOH A:2344 , HOH A:2436 , HOH A:2437 , HOH A:2438BINDING SITE FOR RESIDUE HEM A1431

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X5W)

(-) 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 2X5W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X5W)

(-) Exons   (0, 0)

(no "Exon" information available for 2X5W)

(-) 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:409
 aligned with CP125_MYCTO | P9WPP0 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:409
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418         
          CP125_MYCTO    19 SPNLPPGFDFTDPAIYAERLPVAEFAELRSAAPIWWNGQDPGKGGGFHDGGFWAITKLNDVKEISRHSDVFSSYENGVIPRFKNDIAREDIEVQRFVMLNMDAPHHTRLRKIISRGFTPRAVGRLHDELQERAQKIAAEAAAAGSGDFVEQVSCELPLQAIAGLLGVPQEDRGKLFHWSNEMTGNEDPEYAHIDPKASSAELIGYAMKMAEEKAKNPADDIVTQLIQADIDGEKLSDDEFGFFVVMLAVAGNETTRNSITQGMMAFAEHPDQWELYKKVRPETAADEIVRWATPVTAFQRTALRDYELSGVQIKKGQRVVMFYRSANFDEEVFQDPFTFNILRNPNPHVGFGGTGAHYCIGANLARMTINLIFNAVADHMPDLKPISAPERLRSGWLNGIKHWQVDYTG 427
               SCOP domains d2x5wa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-2x5wA01 A:300-397                                                                            ------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhh.hhhhhhhhhhhh.eeeee............eeeee.hhhhhhhhhhh...ee..............hhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...eeeeee...eee..eee....eeeeehhhhh.................................hhhhhhhhhhhhhhhhhhhh...ee....ee........eee.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x5w A  19 SPNLPPGFDFTDPAIYAERLPVAEFAELRSAAPIWWNGQDPGKGGGFHDGGFWAITKLNDVKEISRHSDVFSSYENGVIPRFKNDIAREDIEVQRFVMLNMDAPHHTRLRKIISRGFTPRAVGRLHDELQERAQKIAAEAAAAGSGDFVEQVSCELPLQAIAGLLGVPQEDRGKLFHWSNEMTGNEDPEYAHIDPKASSAELIGYAMKMAEEKAKNPADDIVTQLIQADIDGEKLSDDEFGFFVVMLAVAGNETTRNSITQGMMAFAEHPDQWELYKKVRPETAADEIVRWATPVTAFQRTALRDYELSGVQIKKGQRVVMFYRSANFDEEVFQDPFTFNILRNPNPHVGFGGTGAHYCIGANLARMTINLIFNAVADHMPDLKPISAPERLRSGWLNGIKHWQVDYTG 427
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418         


Chain A from PDB  Type:PROTEIN  Length:409
 aligned with CP125_MYCTU | P9WPP1 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:409
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418         
          CP125_MYCTU    19 SPNLPPGFDFTDPAIYAERLPVAEFAELRSAAPIWWNGQDPGKGGGFHDGGFWAITKLNDVKEISRHSDVFSSYENGVIPRFKNDIAREDIEVQRFVMLNMDAPHHTRLRKIISRGFTPRAVGRLHDELQERAQKIAAEAAAAGSGDFVEQVSCELPLQAIAGLLGVPQEDRGKLFHWSNEMTGNEDPEYAHIDPKASSAELIGYAMKMAEEKAKNPADDIVTQLIQADIDGEKLSDDEFGFFVVMLAVAGNETTRNSITQGMMAFAEHPDQWELYKKVRPETAADEIVRWATPVTAFQRTALRDYELSGVQIKKGQRVVMFYRSANFDEEVFQDPFTFNILRNPNPHVGFGGTGAHYCIGANLARMTINLIFNAVADHMPDLKPISAPERLRSGWLNGIKHWQVDYTG 427
               SCOP domains d2x5wa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-2x5wA01 A:300-397                                                                            ------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhh.hhhhhhhhhhhh.eeeee............eeeee.hhhhhhhhhhh...ee..............hhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...eeeeee...eee..eee....eeeeehhhhh.................................hhhhhhhhhhhhhhhhhhhh...ee....ee........eee.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x5w A  19 SPNLPPGFDFTDPAIYAERLPVAEFAELRSAAPIWWNGQDPGKGGGFHDGGFWAITKLNDVKEISRHSDVFSSYENGVIPRFKNDIAREDIEVQRFVMLNMDAPHHTRLRKIISRGFTPRAVGRLHDELQERAQKIAAEAAAAGSGDFVEQVSCELPLQAIAGLLGVPQEDRGKLFHWSNEMTGNEDPEYAHIDPKASSAELIGYAMKMAEEKAKNPADDIVTQLIQADIDGEKLSDDEFGFFVVMLAVAGNETTRNSITQGMMAFAEHPDQWELYKKVRPETAADEIVRWATPVTAFQRTALRDYELSGVQIKKGQRVVMFYRSANFDEEVFQDPFTFNILRNPNPHVGFGGTGAHYCIGANLARMTINLIFNAVADHMPDLKPISAPERLRSGWLNGIKHWQVDYTG 427
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418
   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 2X5W)

(-) 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_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.

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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CP125_MYCTO | P9WPP0: 2x5l 2xc3 2xn8 3ivy 3iw0 3iw1 3iw2
        CP125_MYCTU | P9WPP1: 2x5l 2xc3 2xn8 3ivy 3iw0 3iw1 3iw2

(-) Related Entries Specified in the PDB File

2x5l X-RAY STRUCTURE OF THE TRUNCATED FORM OF CYP125A1 FROM M. TUBERCULOSIS