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(-) Description

Title :  QUATERNARY AMMONIUM OXIDATIVE DEMETHYLATION: X-RAY CRYSTALLOGRAPHIC, RESONANCE RAMAN AND UV-VISIBLE SPECTROSCOPIC ANALYSIS OF A RIESKE-TYPE DEMETHYLASE
 
Authors :  K. D. Daughtry, Y. Xiao, D. Stoner-Ma, E. Cho, A. M. Orville, P. Liu, K. N.
Date :  03 Jan 12  (Deposition) - 08 Feb 12  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Rieske-Type, Mononuclear Non-Heme Iron, N-Demethylase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. D. Daughtry, Y. Xiao, D. Stoner-Ma, E. Cho, A. M. Orville, P. Liu, K. N. Allen
Quaternary Ammonium Oxidative Demethylation: X-Ray Crystallographic, Resonance Raman, And Uv-Visible Spectroscopic Analysis Of A Rieske-Type Demethylase.
J. Am. Chem. Soc. V. 134 2823 2012
PubMed-ID: 22224443  |  Reference-DOI: 10.1021/JA2111898

(-) Compounds

Molecule 1 - RING-HYDROXYLATING DIOXYGENASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PASK-IBA5+
    Gene: NP_435646, RA0400, SMA0751
    Organism Common: ENSIFER MELILOTI
    Organism Scientific: SINORHIZOBIUM MELILOTI
    Organism Taxid: 266834
    Strain: 1021

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL1Ligand/IonGLYCEROL
4PRO1Mod. Amino AcidPROLINE
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2FES3Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL3Ligand/IonGLYCEROL
4PRO3Mod. Amino AcidPROLINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:86 , HIS A:88 , ARG A:89 , SER A:91 , CYS A:106 , HIS A:109 , TRP A:111BINDING SITE FOR RESIDUE FES A 501
2AC2SOFTWAREHIS A:204 , HIS A:209 , ASP A:360 , HOH A:887 , HOH A:953 , HOH A:960BINDING SITE FOR RESIDUE FE A 502
3AC3SOFTWAREARG A:14 , ARG A:15 , LEU A:16 , GLU A:22 , HOH A:620 , HOH A:1039BINDING SITE FOR RESIDUE GOL A 503
4AC4SOFTWARETHR A:61 , GLU A:68 , LEU A:92 , LYS A:95 , ARG A:97BINDING SITE FOR RESIDUE PRO A 504

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:202 -A:205

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:289 -Pro A:290
2Tyr A:301 -Pro A:302

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VCA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VCA)

(-) Exons   (0, 0)

(no "Exon" information available for 3VCA)

(-) 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:398
 aligned with Q92ZP9_RHIME | Q92ZP9 from UniProtKB/TrEMBL  Length:412

    Alignment length:403
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405   
         Q92ZP9_RHIME     6 TSIHQRLDRRLSGFSLEQPFYTSPEVYALDLQHIFYKQWLYAVPVCQLAKAGSYTTLRVGAYEVVIVRSRDGEVRAFHNSCRHRGSLICKARQGQVAKLVCPYHQWTYELDGKLIWANDMGPDFDASKYGLKPVNLRNLDGLIYICLSDTPPDFQTFAQLARPYLEVHDLKDAKVAFTSTIIEKGNWKLVWENNRECYHCSSNHPALCRSFPLDPEVAGVQADGGVSKKLQAHFDRCEAAGTPAQFVLAGDGQYRLARMPLQEKALSYTMDGKAAVSRHLGRVAPPDAGTLLMFHYPSTWNHFLPDHSLTFRVMPISPTETEVTTTWLVHKDAVEGVDYDLKRLTEVWIATNDEDREIVETNQQGILSPAYVPGPYSPGQESGVMQFVDWYAASLERALAPRQ 408
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeeee.hhhh...eeeeeee..eeeeeee.....eeeee..............eee...ee......ee.....eee........hhhhh...eeeeeee..eeeee.......hhhhhhhhhhhhhhhhhh.eeeeeeeeeee..hhhhhhhhhh...hhhhhhhhhhh....hhhhhh.----..hhhhhhhhhhhhhh......ee.....eeeeee..............................eeeeee...eeeee....eeeeeeeeee..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhh.-. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vca A   6 TSIHQRLDRRLSGFSLEQPFYTSPEVYALDLQHIFYKQWLYAVPVCQLAKAGSYTTLRVGAYEVVIVRSRDGEVRAFHNSCRHRGSLICKARQGQVAKLVCPYHQWTYELDGKLIWANDMGPDFDASKYGLKPVNLRNLDGLIYICLSDTPPDFQTFAQLARPYLEVHDLKDAKVAFTSTIIEKGNWKLVWENNRECYHCSSNHPALCRSFPLDPEVAGV----GVSKKLQAHFDRCEAAGTPAQFVLAGDGQYRLARMPLQEKALSYTMDGKAAVSRHLGRVAPPDAGTLLMFHYPSTWNHFLPDHSLTFRVMPISPTETEVTTTWLVHKDAVEGVDYDLKRLTEVWIATNDEDREIVETNQQGILSPAYVPGPYSPGQESGVMQFVDWYAASLERALAP-P 504
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225    |  235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405| |
                                                                                                                                                                                                                                                     225  230                                                                                                                                                                             406 |
                                                                                                                                                                                                                                                                                                                                                                                                                                            504
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3VCA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VCA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VCA)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q92ZP9_RHIME | Q92ZP9)
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:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    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: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: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:0016708    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donor    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from NADH or NADPH and one other donor, and two atoms of oxygen are incorporated into one donor.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
    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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        Q92ZP9_RHIME | Q92ZP9: 3vcp 4qup 4quq 4qur 5hl4

(-) Related Entries Specified in the PDB File

3vcp