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(-) Description

Title :  X-RAY STRUCTURE OF THE SUBSTRATE-FREE MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 CYP124
 
Authors :  J. B. Johnston, P. M. Kells, L. M. Podust, P. R. Ortiz De Montellano
Date :  30 Jun 09  (Deposition) - 06 Oct 09  (Release) - 07 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Metal-Binding, Oxidoreductase, Omega-Hydroxylation, P450, Iron, Heme, Fatty Acid, Monooxygenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Johnston, P. M. Kells, L. M. Podust, P. R. Ortiz De Montellano
Biochemical And Structural Characterization Of Cyp124: A Methyl-Branched Lipid {Omega}- Hydroxylase From Mycobacterium Tuberculosis.
Proc. Natl. Acad. Sci. Usa V. 106 20687 2009
PubMed-ID: 19933331  |  Reference-DOI: 10.1073/PNAS.0907398106

(-) Compounds

Molecule 1 - PUTATIVE CYTOCHROME P450 124
    Chains: A
    EC Number: 1.14.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCWORI
    Expression System Strain: DH5A
    Expression System Taxid: 562
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: CYP124

 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:110 , ILE A:111 , HIS A:118 , ARG A:122 , LEU A:263 , ALA A:267 , GLY A:268 , THR A:271 , THR A:272 , ARG A:320 , TYR A:343 , GLY A:370 , PHE A:371 , GLY A:372 , ALA A:376 , HIS A:377 , CYS A:379 , GLY A:381 , LEU A:384 , ALA A:385 , GLU A:388 , HOH A:2239 , HOH A:2288 , HOH A:2308 , HOH A:2346 , HOH A:2347BINDING SITE FOR RESIDUE HEM A 450

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WM5)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr A:91 -Pro A:92
2Asp A:115 -Pro A:116
3Asn A:364 -Pro A:365

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WM5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WM5)

(-) Exons   (0, 0)

(no "Exon" information available for 2WM5)

(-) 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:425
 aligned with CP124_MYCTO | P9WPP2 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:428
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420        
          CP124_MYCTO     1 MGLNTAIATRVNGTPPPEVPIAGIELGSLDFWALDDDVRDGAFATLRREAPISFWPTIELPGFVAGNGHWALTKNDDVFYASRHPDIFSSYPNITINDQTPELAEYFGSMIVLDDPRHQRLRSIVSRAFTPKVVARIEAAVRDRAHRLVSSMIANNPDRQADLVSELAGPLPLQIICDMMGIPKADHQRIFHWTNVILGFGDPDLATDFDEFMQVSADIGAYATALAEDRRVNHHDDLTSSLVEAEVDGERLSSREIASFFILLVVAGNETTRNAITHGVLALSRYPEQRDRWWSDFDGLAPTAVEEIVRWASPVVYMRRTLTQDIELRGTKMAAGDKVSLWYCSANRDESKFADPWTFDLARNPNPHLGFGGGGAHFCLGANLARREIRVAFDELRRQMPDVVATEEPARLLSQFIHGIKTLPVTWS 428
               SCOP domains d2wm5a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-2wm5A01 A:300-398                                                                             ------------------------------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-2wm5A02 A:300-398                                                                             ------------------------------ Pfam domains (2)
         Sec.struct. author ...................hhhhh...hhhhhh.hhhhhh.hhhhhhhhh.eee......---......eee.hhhhhhhhhhh...ee..........hhhhhhhh.hhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeehhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....eeeee...ee....ee....eeeehhhhhh..................................hhhhhhhhhhhhhhhhhhh...ee..................eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wm5 A   1 MGLNTAIATRVNGTPPPEVPIADIELGSLDFWALDDDVRDGAFATLRREAPISFWPTIEL---VAGNGHWALTKYDDVFYASRHPDIFSSYPNITINDQTPELAEYFGSMIVLDDPRHQRLRSIVSRAFTPKVVARIEAAVRDRAHRLVSSMIANNPDRQADLVSELAGPLPLQIICDMMGIPKADHQRIFHWTNVILGFGDPDLATDFDEFMQVSADIGAYATALAEDRRVNHHDDLTSSLVEAEVDGERLSSREIASFFILLVVAGNETTRNAITHGVLALSRYPEQRDRWWSDFDGLAPTAVEEIVRWASPVVYMRRTLTQDIELRGTKMAAGDKVSLWYCSANRDESKFADPWTFDLARNPNPHLGFGGGGAHFCLGANLARREIRVAFDELRRQMPDVVATEEPARLLSQFIHGIKTLPVTWS 428
                                    10        20        30        40        50        60   |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420        
                                                                                      60  64                                                                                                                                                                                                                                                                                                                                                                            


Chain A from PDB  Type:PROTEIN  Length:425
 aligned with CP124_MYCTU | P9WPP3 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:428
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420        
          CP124_MYCTU     1 MGLNTAIATRVNGTPPPEVPIADIELGSLDFWALDDDVRDGAFATLRREAPISFWPTIELPGFVAGNGHWALTKYDDVFYASRHPDIFSSYPNITINDQTPELAEYFGSMIVLDDPRHQRLRSIVSRAFTPKVVARIEAAVRDRAHRLVSSMIANNPDRQADLVSELAGPLPLQIICDMMGIPKADHQRIFHWTNVILGFGDPDLATDFDEFMQVSADIGAYATALAEDRRVNHHDDLTSSLVEAEVDGERLSSREIASFFILLVVAGNETTRNAITHGVLALSRYPEQRDRWWSDFDGLAPTAVEEIVRWASPVVYMRRTLTQDIELRGTKMAAGDKVSLWYCSANRDESKFADPWTFDLARNPNPHLGFGGGGAHFCLGANLARREIRVAFDELRRQMPDVVATEEPARLLSQFIHGIKTLPVTWS 428
               SCOP domains d2wm5a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-2wm5A01 A:300-398                                                                             ------------------------------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------p450-2wm5A02 A:300-398                                                                             ------------------------------ Pfam domains (2)
         Sec.struct. author ...................hhhhh...hhhhhh.hhhhhh.hhhhhhhhh.eee......---......eee.hhhhhhhhhhh...ee..........hhhhhhhh.hhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeehhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....eeeee...ee....ee....eeeehhhhhh..................................hhhhhhhhhhhhhhhhhhh...ee..................eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wm5 A   1 MGLNTAIATRVNGTPPPEVPIADIELGSLDFWALDDDVRDGAFATLRREAPISFWPTIEL---VAGNGHWALTKYDDVFYASRHPDIFSSYPNITINDQTPELAEYFGSMIVLDDPRHQRLRSIVSRAFTPKVVARIEAAVRDRAHRLVSSMIANNPDRQADLVSELAGPLPLQIICDMMGIPKADHQRIFHWTNVILGFGDPDLATDFDEFMQVSADIGAYATALAEDRRVNHHDDLTSSLVEAEVDGERLSSREIASFFILLVVAGNETTRNAITHGVLALSRYPEQRDRWWSDFDGLAPTAVEEIVRWASPVVYMRRTLTQDIELRGTKMAAGDKVSLWYCSANRDESKFADPWTFDLARNPNPHLGFGGGGAHFCLGANLARREIRVAFDELRRQMPDVVATEEPARLLSQFIHGIKTLPVTWS 428
                                    10        20        30        40        50        60   |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420        
                                                                                      60  64
   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 2WM5)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (16, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CP124_MYCTU | P9WPP3)
molecular function
    GO:0070402    NADPH binding    Interacting selectively and non-covalently with the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
    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:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0010430    fatty acid omega-oxidation    A fatty acid oxidation process in which the methyl group at the end of the fatty acid molecule (the omega carbon) is first oxidized to a hydroxyl group, then to an oxo group, and finally to a carboxyl group. The long chain dicarboxylates derived from omega-oxidation then enter the beta-oxidation pathway for further degradation.
    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:0097089    methyl-branched fatty acid metabolic process    The chemical reactions and pathways involving methyl-branched fatty acids, aliphatic monocarboxylic acids with methyl branches on the main chain.
    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   (CP124_MYCTO | P9WPP2)
molecular function
    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:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    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.

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  CP124_MYCTO | P9WPP2
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 Related Entries

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

UniProtKB/Swiss-Prot
        CP124_MYCTO | P9WPP2: 2wm4
        CP124_MYCTU | P9WPP3: 2wm4

(-) Related Entries Specified in the PDB File

2wm4 BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF CYP124: A METHYL-BRANCHED LIPID OMEGA- HYDROXYLASE FROM MYCOBACTERIUM TUBERCULOSIS