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(-) Description

Title :  THE CRYSTAL STRUCTURE OF NITROBENZENE DIOXYGENASE IN COMPLEX WITH 3-NITROTOLUENE
 
Authors :  R. Friemann, M. M. Ivkovic-Jensen, D. J. Lessner, C. Yu, D. T. Gibson, R. E. Parales, H. Eklund, S. Ramaswamy
Date :  15 Mar 05  (Deposition) - 04 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Nitrobenzene Dioxygenase, Crystal Structure, Nitroarene, Rieske Non-Heme Dioxygenase, Substrate Specificity Iron- Sulfur, Metal-Binding, Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Friemann, M. M. Ivkovic-Jensen, D. J. Lessner, C. Yu, D. T. Gibson, R. E. Parales, H. Eklund, S. Ramaswamy
Structural Insight Into The Dioxygenation Of Nitroarene Compounds: The Crystal Structure Of Nitrobenzene Dioxygenase
J. Mol. Biol. V. 348 1139 2005
PubMed-ID: 15854650  |  Reference-DOI: 10.1016/J.JMB.2005.03.052

(-) Compounds

Molecule 1 - OXYGENASE-ALPHA NBDO
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDTG927
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 562
    Expression System Vector: PUC18
    Organism Scientific: COMAMONAS SP.
    Organism Taxid: 58226
    Other Details: WASTE TREATMENT PLANT IN NEW JERSEY. (SF NISHINO AND JC SPAIN. 1995. APPL. ENVIRON. MICROBIOL. 61:2308-2313)
    Strain: JS765
    Synonym: NITROBENZENE DIOXYGENASE
 
Molecule 2 - OXYGENASE-BETA NBDO
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDTG927
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 562
    Expression System Vector: PUC18
    Organism Scientific: COMAMONAS SP.
    Organism Taxid: 58226
    Other Details: WASTE TREATMENT PLANT IN NEW JERSEY. (SF NISHINO AND JC SPAIN. 1995. APPL. ENVIRON. MICROBIOL. 61:2308-2313)
    Strain: JS765
    Synonym: NITROBENZENE DIOXYGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 20)

Asymmetric Unit (6, 20)
No.NameCountTypeFull Name
13NT1Ligand/Ion3-NITROTOLUENE
2EDO6Ligand/Ion1,2-ETHANEDIOL
3EOH9Ligand/IonETHANOL
4FE1Ligand/IonFE (III) ION
5FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
6NI2Ligand/IonNICKEL (II) ION
Biological Unit 1 (4, 51)
No.NameCountTypeFull Name
13NT3Ligand/Ion3-NITROTOLUENE
2EDO18Ligand/Ion1,2-ETHANEDIOL
3EOH27Ligand/IonETHANOL
4FE-1Ligand/IonFE (III) ION
5FES3Ligand/IonFE2/S2 (INORGANIC) CLUSTER
6NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:206 , HIS A:211 , ASP A:360 , HOH A:2230 , HOH A:2422BINDING SITE FOR RESIDUE FE A1441
02AC2SOFTWAREHIS B:14 , GLU B:18 , GLU B:160 , HOH B:2047 , HOH B:2048 , HOH B:2259BINDING SITE FOR RESIDUE NI B1195
03AC3SOFTWAREHIS B:56 , EDO B:1198 , HOH B:2002 , HOH B:2013 , HOH B:2130BINDING SITE FOR RESIDUE NI B1196
04AC4SOFTWARECYS A:79 , HIS A:81 , ARG A:82 , CYS A:99 , TYR A:101 , HIS A:102 , TRP A:104BINDING SITE FOR RESIDUE FES A1440
05AC5SOFTWAREASN A:199 , PHE A:200 , ASP A:203 , ASN A:258 , PHE A:293 , ASN A:295 , HOH A:2422BINDING SITE FOR RESIDUE 3NT A1442
06AC6SOFTWAREPRO A:47 , SER A:48 , ASP A:51 , HOH A:2048 , HOH A:2423 , ARG B:78 , TYR B:79 , GLN B:80BINDING SITE FOR RESIDUE EDO A1443
07AC7SOFTWARELYS A:30 , ARG A:35 , ASP A:151 , SER A:425 , HOH A:2424BINDING SITE FOR RESIDUE EDO A1444
08AC8SOFTWAREVAL A:53 , LYS A:54 , GLU A:90 , PRO A:184 , LYS A:186 , EOH A:1446 , EOH A:1447 , GLU B:70 , ARG B:183BINDING SITE FOR RESIDUE EDO A1445
09AC9SOFTWARETYR B:88 , GLN B:102 , LEU B:191 , VAL B:192 , PHE B:193 , HOH B:2296 , HOH B:2297BINDING SITE FOR RESIDUE EDO B1197
10BC1SOFTWARETYR A:174 , MET B:2 , ASN B:4 , GLU B:7 , HIS B:56 , NI B:1196 , HOH B:2002 , HOH B:2013 , HOH B:2130 , HOH B:2298 , HOH B:2299BINDING SITE FOR RESIDUE EDO B1198
11BC2SOFTWARETHR B:35 , VAL B:120 , ASN B:122 , HOH B:2300BINDING SITE FOR RESIDUE EDO B1199
12BC3SOFTWAREVAL A:53 , PRO A:183 , PRO A:184 , TYR A:327 , EDO A:1445 , HOH A:2323 , GLU B:70 , HOH B:2160BINDING SITE FOR RESIDUE EOH A1446
13BC4SOFTWARELYS A:54 , LYS A:56 , GLU A:61 , GLU A:90 , LYS A:186 , TRP A:325 , EDO A:1445 , GLU B:149 , HOH B:2241BINDING SITE FOR RESIDUE EOH A1447
14BC5SOFTWARESER A:141 , PHE A:142 , HIS A:143 , HOH A:2179 , HOH A:2425 , GLU B:17BINDING SITE FOR RESIDUE EOH A1448
15BC6SOFTWAREHIS A:88 , ALA A:89 , HOH A:2050 , ASN B:111 , HOH B:2205BINDING SITE FOR RESIDUE EOH A1449
16BC7SOFTWAREGLU A:153 , ALA A:154 , PRO A:155 , GLU A:431 , HOH A:2409 , GLN B:80BINDING SITE FOR RESIDUE EOH A1450
17BC8SOFTWARELEU B:71 , PRO B:112 , LYS B:113 , ALA B:146 , ARG B:147 , ARG B:148BINDING SITE FOR RESIDUE EOH B1200
18BC9SOFTWAREARG B:115 , PHE B:116 , THR B:158 , HOH B:2215 , HOH B:2302BINDING SITE FOR RESIDUE EOH B1201
19CC1SOFTWAREGLU B:55 , HIS B:56 , LYS B:172BINDING SITE FOR RESIDUE EOH B1202
20CC2SOFTWARETRP A:166 , ARG A:286 , HOH A:2295 , ASN B:4 , GLN B:6BINDING SITE FOR RESIDUE EOH B1203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:182 -Pro A:183
2Phe A:299 -Pro A:300
3Asn B:111 -Pro B:112

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BMR)

(-) 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:437
 aligned with Q8RTL4_9BURK | Q8RTL4 from UniProtKB/TrEMBL  Length:447

    Alignment length:437
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       
         Q8RTL4_9BURK     3 YQNLVSEAGLTQKLLIHGDKELFQHELKTIFARNWLFLTHDSLIPSPGDYVKAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVHAEAGNAKGFVCGYHGWGYGSNGELQSVPFEKELYGDAIKKKCLGLKEVPRIESFHGFIYGCFDAEAPPLIDYLGDAAWYLEPTFKYSGGLELVGPPGKVVVKANWKSFAENFVGDGYHVGWTHAAALRAGQSVFSSIAGNAKLPPEGAGLQMTSKYGSGMGVFWGYYSGNFSADMIPDLMAFGAAKQEKLAKEIGDVRARIYRSFLNGTIFPNNSFLTGSAAFRVWNPIDENTTEVWTYAFVEKDMPEDLKRRVADAVQRSIGPAGFWESDDNENMETMSQNGKKYQSSNIDQIASLGFGKDVYGDECYPGVVGKSAIGETSYRGFYRAYQAHISSSNWAEFENASRNWHI 439
               SCOP domains d2bmra1 A:3-152 Nitrobenzene dioxygenase alpha subunit, NBDO-alpha                                                                                    d2bmra2 A:153-439 Nitrobenzene dioxygenase alpha subunit, NBDO-alpha                                                                                                                                                                                                                            SCOP domains
               CATH domains 2bmrA01 A:3-33,A:163-439       2bmrA02 A:34-162 'Rieske'-like iron-sulphur domains                                                                              2bmrA01 A:3-33,A:163-439 Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhh.eee.hhhhhhhhhhhhhhhh.....eeeee.hhh....eeeeeee..eeeeeee.....eeeee..............eee..eee......eee....eee..hhhhhhhhhhhhhhh......eeeee..eeeee......hhhhhhhhhhhhhhhhhh....eeeeeeeeeeee..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh........eeee.....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...eeee....eeeeeeeee..eeeeeeeeeee...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhh.eee........ee.......eee.....hhhhhhhhhhhhhhhh..hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bmr A   3 YQNLVSEAGLTQKLLIHGDKELFQHELKTIFARNWLFLTHDSLIPSPGDYVKAKMGVDEVIVSRQNDGSVRAFLNVCRHRGKTLVHAEAGNAKGFVCGYHGWGYGSNGELQSVPFEKELYGDAIKKKCLGLKEVPRIESFHGFIYGCFDAEAPPLIDYLGDAAWYLEPTFKYSGGLELVGPPGKVVVKANWKSFAENFVGDGYHVGWTHAAALRAGQSVFSSIAGNAKLPPEGAGLQMTSKYGSGMGVFWGYYSGNFSADMIPDLMAFGAAKQEKLAKEIGDVRARIYRSFLNGTIFPNNSFLTGSAAFRVWNPIDENTTEVWTYAFVEKDMPEDLKRRVADAVQRSIGPAGFWESDDNENMETMSQNGKKYQSSNIDQIASLGFGKDVYGDECYPGVVGKSAIGETSYRGFYRAYQAHISSSNWAEFENASRNWHI 439
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       


Chain B from PDB  Type:PROTEIN  Length:194
 aligned with Q8RTL3_9BURK | Q8RTL3 from UniProtKB/TrEMBL  Length:194

    Alignment length:194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    
         Q8RTL3_9BURK     1 MMINTQEDKLVSAHDAEEFHRFFVGHDSDLQQEVTTLLTREAHLLDIQAYKAWLEHFVAPEIKYQVISRELRSTSERRYQLNDAVNLYNENYQQLKVRVEHQMDPQNWANNPKIRFTRFVTNVTAAKDKSAPEILHVRSNLILHRARRENQVDVFYATREDKWKRIEGGGIKLVERFVDYPERIPQTHNLLVFL 194
               SCOP domains d2bmrb_ B: automated matches                                                                                                                                                                       SCOP domains
               CATH domains 2bmrB00 B:1-194  [code=3.10.450.50, no name defined]                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhheeeeeeeeeeee..............eeeeeeehhhhhhhhhhhhhh..hhhhh...eeeeeeeeeeeee......eeeeeeeeeeeeee...eeeeeeeeeeeeeee.....eeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bmr B   1 MMINTQEDKLVSAHDAEEFHRFFVGHDSDLQQEVTTLLTREAHLLDIQAYKAWLEHFVAPEIKYQVISRELRSTSERRYQLNDAVNLYNENYQQLKVRVEHQMDPQNWANNPKIRFTRFVTNVTAAKDKSAPEILHVRSNLILHRARRENQVDVFYATREDKWKRIEGGGIKLVERFVDYPERIPQTHNLLVFL 194
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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  (3, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BMR)

(-) Gene Ontology  (12, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8RTL4_9BURK | Q8RTL4)
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: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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.

Chain B   (Q8RTL3_9BURK | Q8RTL3)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    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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 Related Entries

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

UniProtKB/TrEMBL
        Q8RTL3_9BURK | Q8RTL3: 2bmo 2bmq
        Q8RTL4_9BURK | Q8RTL4: 2bmo 2bmq

(-) Related Entries Specified in the PDB File

2bmo THE CRYSTAL STRUCTURE OF NITROBENZENE DIOXYGENASE
2bmq THE CRYSTAL STRUCTURE OF NITROBENZENE DIOXYGENASE IN COMPLEX WITH NITROBENZENE