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(-) Description

Title :  ETHYLENE GLYCOL-BOUND FORM OF P450 CYP125A3 FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  D. J. Frank, E. Garcia Fernandez, P. M. Kells, J. L. Garcia Lopez, L. M. P. R. Ortiz De Montellano
Date :  09 Apr 12  (Deposition) - 27 Feb 13  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase, Cholesterol Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Garcia-Fernandez, D. J. Frank, B. Galan, P. M. Kells, L. M. Podust, J. L. Garcia, P. R. Ortiz De Montellano
A Highly Conserved Mycobacterial Cholesterol Catabolic Pathway.
Environ. Microbiol. V. 15 2342 2013
PubMed-ID: 23489718  |  Reference-DOI: 10.1111/1462-2920.12108

(-) Compounds

Molecule 1 - P450 HEME-THIOLATE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCW
    Expression System Strain: DH5[ALPHA]
    Expression System Taxid: 668369
    Expression System Vector Type: PLASMID
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 1772
    Strain: MC2 155
    Synonym: CYP125A3

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO11Ligand/Ion1,2-ETHANEDIOL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO22Ligand/Ion1,2-ETHANEDIOL
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:20 , LYS A:63 , PRO A:348 , HIS A:349 , THR A:355 , HOH A:2095BINDING SITE FOR RESIDUE EDO A1416
02AC2SOFTWARETYR A:277 , ARG A:281 , PRO A:282 , GLU A:283 , ASN A:371 , ASN A:375BINDING SITE FOR RESIDUE EDO A1417
03AC3SOFTWARELEU A:99 , LEU A:100 , HIS A:107 , ARG A:111 , ALA A:251 , GLY A:252 , THR A:255 , THR A:256 , PRO A:295 , PHE A:299 , ARG A:301 , TYR A:324 , GLY A:351 , PHE A:352 , GLY A:353 , GLY A:354 , ALA A:357 , HIS A:358 , CYS A:360 , ILE A:361 , GLY A:362 , EDO A:1423 , HOH A:2105 , HOH A:2277 , HOH A:2314BINDING SITE FOR RESIDUE HEM A1418
04AC4SOFTWAREHIS A:262 , ARG A:392 , HOH A:2245BINDING SITE FOR RESIDUE EDO A1419
05AC5SOFTWAREVAL A:24 , TRP A:292 , HIS A:338 , HOH A:2272 , HOH A:2296BINDING SITE FOR RESIDUE EDO A1420
06AC6SOFTWAREILE A:80 , PHE A:299 , EDO A:1423 , HOH A:2135BINDING SITE FOR RESIDUE EDO A1421
07AC7SOFTWARESER A:75 , PRO A:76 , ASP A:93 , ARG A:96 , HOH A:2134BINDING SITE FOR RESIDUE EDO A1422
08AC8SOFTWAREMET A:247 , ALA A:251 , HEM A:1418 , EDO A:1421BINDING SITE FOR RESIDUE EDO A1423
09AC9SOFTWARECYS A:155 , GLU A:156 , ASN A:181 , HOH A:2211BINDING SITE FOR RESIDUE EDO A1424
10BC1SOFTWAREASP A:195 , PRO A:196 , ALA A:197 , MET A:198BINDING SITE FOR RESIDUE EDO A1425
11BC2SOFTWAREPHE A:10 , ASP A:11 , ASP A:14 , HOH A:2030BINDING SITE FOR RESIDUE EDO A1427

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:104 -Pro A:105
2Ser A:345 -Pro A:346

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4APY)

(-) 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:414
 aligned with CP125_MYCS2 | A0R4Y3 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:414
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411    
          CP125_MYCS2     2 PTPNIPSDFDFLDATLNLERLPVEELAELRKSEPIHWVDVPGGTGGFGDKGYWLVTKHADVKEVSRRSDVFGSSPDGAIPVWPQDMTREAVDLQRAVLLNMDAPQHTRLRKIISRGFTPRAIGRLEDELRSRAQKIAQTAAAQGAGDFVEQVSCELPLQAIAELLGVPQDDRDKLFRWSNEMTAGEDPEYADVDPAMSSFELISYAMKMAEERAVNPTEDIVTKLIEADIDGEKLSDDEFGFFVVMLAVAGNETTRNSITHGMIAFAQNPDQWELYKKERPETAADEIVRWATPVSAFQRTALEDVELGGVQIKKGQRVVMSYRSANFDEEVFEDPHTFNILRSPNPHVGFGGTGAHYCIGANLARMTINLIFNAIADNMPDLKPIGAPERLKSGWLNGIKHWQVDYTGAGKAS 415
               SCOP domains d4apya_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhhhhh.hhhhhhhhhhhh.eeeee...........eeeee.hhhhhhhhhhh...ee..............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...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
                 4apy A   2 PTPNIPSDFDFLDATLNLERLPVEELAELRKSEPIHWVDVPGGTGGFGDKGYWLVTKHADVKEVSRRSDVFGSSPDGAIPVWPQDMTREAVDLQRAVLLNMDAPQHTRLRKIISRGFTPRAIGRLEDELRSRAQKIAQTAAAQGAGDFVEQVSCELPLQAIAELLGVPQDDRDKLFRWSNEMTAGEDPEYADVDPAMSSFELISYAMKMAEERAVNPTEDIVTKLIEADIDGEKLSDDEFGFFVVMLAVAGNETTRNSITHGMIAFAQNPDQWELYKKERPETAADEIVRWATPVSAFQRTALEDVELGGVQIKKGQRVVMSYRSANFDEEVFEDPHTFNILRSPNPHVGFGGTGAHYCIGANLARMTINLIFNAIADNMPDLKPIGAPERLKSGWLNGIKHWQVDYTGAGKAS 415
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (CP125_MYCS2 | A0R4Y3)
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: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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        CP125_MYCS2 | A0R4Y3: 5dqn

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