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(-) Description

Title :  NAPHTHALENE 1,2-DIOXYGENASE, FULLY REDUCED FORM
 
Authors :  A. Karlsson, J. V. Parales, R. E. Parales, D. T. Gibson, H. Eklund, S. Ramaswamy
Date :  14 Nov 02  (Deposition) - 20 Feb 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Oxidoreductase, Non-Heme Iron Dioxygenase, Enzyme-Substrate Complex, Iron-Sulfur, Aromatic Hydrocarbon Catabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Karlsson, J. V. Parales, R. E. Parales, D. T. Gibson, H. Eklund, S. Ramaswamy
Crystal Structure Of Naphthalene Dioxygenase: Side-On Binding Of Dioxygen To Iron
Science V. 299 1039 2003
PubMed-ID: 12586937  |  Reference-DOI: 10.1126/SCIENCE.1078020

(-) Compounds

Molecule 1 - NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT
    ChainsA
    EC Number1.14.12.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDTG141
    Expression System StrainJM109(DE3)
    Expression System Taxid562
    Organism ScientificPSEUDOMONAS PUTIDA
    Organism Taxid303
    StrainNCIB 9816-4
    SynonymNAPHTHALENE 1,2-DIOXYGENASE ISP ALPHA, NDOB, NAHAC
 
Molecule 2 - NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT
    ChainsB
    EC Number1.14.12.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDTG141
    Expression System StrainJM109(DE3)
    Expression System Taxid562
    Organism ScientificPSEUDOMONAS PUTIDA
    Organism Taxid303
    StrainNCIB 9816-4
    SynonymNAPHTHALENE 1,2-DIOXYGENASE ISP BETA, NDOC, NAHAD

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2FE1Ligand/IonFE (III) ION
3FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
4SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 30)
No.NameCountTypeFull Name
1EDO18Ligand/Ion1,2-ETHANEDIOL
2FE-1Ligand/IonFE (III) ION
3FES3Ligand/IonFE2/S2 (INORGANIC) CLUSTER
4SO49Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:128 , ASN A:129 , LYS A:130 , LYS A:131BINDING SITE FOR RESIDUE SO4 A1451
02AC2SOFTWAREHIS A:208 , HIS A:213 , ASP A:362 , HOH A:2144BINDING SITE FOR RESIDUE FE A1453
03AC3SOFTWAREGLN B:563 , GLN B:565 , HOH B:2054 , HOH B:2125BINDING SITE FOR RESIDUE SO4 B1697
04AC4SOFTWAREGLY B:559 , SER B:560 , GLU B:561 , GLU B:667 , LYS B:672BINDING SITE FOR RESIDUE SO4 B1698
05AC5SOFTWARELEU A:31 , PHE A:35 , MET A:59 , GLY A:60 , ILE A:61 , ASP A:62 , PHE A:152 , TYR A:376 , GLN A:377BINDING SITE FOR RESIDUE EDO A1448
06AC6SOFTWAREHIS A:18 , VAL A:80 , CYS A:81 , ARG A:82 , SER A:381 , ASP A:382 , HOH A:2251 , HOH A:2252BINDING SITE FOR RESIDUE EDO A1449
07AC7SOFTWAREARG A:342 , ASP A:346 , HOH A:2138 , ASN B:582BINDING SITE FOR RESIDUE EDO A1450
08AC8SOFTWARECYS A:81 , HIS A:83 , ARG A:84 , CYS A:101 , TYR A:103 , HIS A:104 , TRP A:106BINDING SITE FOR RESIDUE FES A1452
09AC9SOFTWARETYR B:588 , GLN B:602 , MET B:691 , VAL B:692 , PHE B:693 , HOH B:2123 , HOH B:2124BINDING SITE FOR RESIDUE EDO B1695
10BC1SOFTWAREALA A:50 , ASP A:53 , HOH A:2044 , ARG B:578 , TYR B:579 , LYS B:580 , LEU B:581BINDING SITE FOR RESIDUE EDO B1696
11BC2SOFTWAREARG B:638 , ALA B:658 , GLU B:660 , PHE B:677 , VAL B:678 , ASP B:679 , HOH B:2107 , HOH B:2126BINDING SITE FOR RESIDUE EDO B1699

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O7W)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:184 -Pro A:185
2Phe A:301 -Pro A:302
3Ser B:611 -Pro B:612

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (23, 23)

Asymmetric Unit (23, 23)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_NDOB_PSEPU_001 *N4KNDOB_PSEPU  ---  ---AN4K
02UniProtVAR_NDOB_PSEPU_002 *S12FNDOB_PSEPU  ---  ---AS12F
03UniProtVAR_NDOB_PSEPU_003 *S15TNDOB_PSEPU  ---  ---AS15T
04UniProtVAR_NDOB_PSEPU_004 *K32RNDOB_PSEPU  ---  ---AK32R
05UniProtVAR_NDOB_PSEPU_005 *A50SNDOB_PSEPU  ---  ---AA50S
06UniProtVAR_NDOB_PSEPU_006 *N70SNDOB_PSEPU  ---  ---AN70S
07UniProtVAR_NDOB_PSEPU_007 *D122ENDOB_PSEPU  ---  ---AD122E
08UniProtVAR_NDOB_PSEPU_008 *M173INDOB_PSEPU  ---  ---AM173I
09UniProtVAR_NDOB_PSEPU_009 *S225ANDOB_PSEPU  ---  ---AS225A
10UniProtVAR_NDOB_PSEPU_010 *S225CNDOB_PSEPU  ---  ---AS225C
11UniProtVAR_NDOB_PSEPU_011 *A232VNDOB_PSEPU  ---  ---AA232V
12UniProtVAR_NDOB_PSEPU_012 *A275SNDOB_PSEPU  ---  ---AA275S
13UniProtVAR_NDOB_PSEPU_013 *E391KNDOB_PSEPU  ---  ---AE391K
14UniProtVAR_NDOB_PSEPU_014 *Q421RNDOB_PSEPU  ---  ---AQ421R
15UniProtVAR_NDOB_PSEPU_015 *H434DNDOB_PSEPU  ---  ---AH434D
16UniProtVAR_NDOC_PSEPU_001 *E17QNDOC_PSEPU  ---  ---BE517Q
17UniProtVAR_NDOC_PSEPU_002 *I19FNDOC_PSEPU  ---  ---BI519F
18UniProtVAR_NDOC_PSEPU_003 *S28ANDOC_PSEPU  ---  ---BS528A
19UniProtVAR_NDOC_PSEPU_004 *V99INDOC_PSEPU  ---  ---BV599I
20UniProtVAR_NDOC_PSEPU_005 *G109SNDOC_PSEPU  ---  ---BG609S
21UniProtVAR_NDOC_PSEPU_006 *M127RNDOC_PSEPU  ---  ---BM627R
22UniProtVAR_NDOC_PSEPU_007 *N130DNDOC_PSEPU  ---  ---BN630D
23UniProtVAR_NDOC_PSEPU_008 *K132ENDOC_PSEPU  ---  ---BK632E
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (23, 69)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_NDOB_PSEPU_001 *N4KNDOB_PSEPU  ---  ---AN4K
02UniProtVAR_NDOB_PSEPU_002 *S12FNDOB_PSEPU  ---  ---AS12F
03UniProtVAR_NDOB_PSEPU_003 *S15TNDOB_PSEPU  ---  ---AS15T
04UniProtVAR_NDOB_PSEPU_004 *K32RNDOB_PSEPU  ---  ---AK32R
05UniProtVAR_NDOB_PSEPU_005 *A50SNDOB_PSEPU  ---  ---AA50S
06UniProtVAR_NDOB_PSEPU_006 *N70SNDOB_PSEPU  ---  ---AN70S
07UniProtVAR_NDOB_PSEPU_007 *D122ENDOB_PSEPU  ---  ---AD122E
08UniProtVAR_NDOB_PSEPU_008 *M173INDOB_PSEPU  ---  ---AM173I
09UniProtVAR_NDOB_PSEPU_009 *S225ANDOB_PSEPU  ---  ---AS225A
10UniProtVAR_NDOB_PSEPU_010 *S225CNDOB_PSEPU  ---  ---AS225C
11UniProtVAR_NDOB_PSEPU_011 *A232VNDOB_PSEPU  ---  ---AA232V
12UniProtVAR_NDOB_PSEPU_012 *A275SNDOB_PSEPU  ---  ---AA275S
13UniProtVAR_NDOB_PSEPU_013 *E391KNDOB_PSEPU  ---  ---AE391K
14UniProtVAR_NDOB_PSEPU_014 *Q421RNDOB_PSEPU  ---  ---AQ421R
15UniProtVAR_NDOB_PSEPU_015 *H434DNDOB_PSEPU  ---  ---AH434D
16UniProtVAR_NDOC_PSEPU_001 *E17QNDOC_PSEPU  ---  ---BE517Q
17UniProtVAR_NDOC_PSEPU_002 *I19FNDOC_PSEPU  ---  ---BI519F
18UniProtVAR_NDOC_PSEPU_003 *S28ANDOC_PSEPU  ---  ---BS528A
19UniProtVAR_NDOC_PSEPU_004 *V99INDOC_PSEPU  ---  ---BV599I
20UniProtVAR_NDOC_PSEPU_005 *G109SNDOC_PSEPU  ---  ---BG609S
21UniProtVAR_NDOC_PSEPU_006 *M127RNDOC_PSEPU  ---  ---BM627R
22UniProtVAR_NDOC_PSEPU_007 *N130DNDOC_PSEPU  ---  ---BN630D
23UniProtVAR_NDOC_PSEPU_008 *K132ENDOC_PSEPU  ---  ---BK632E
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIESKEPS51296 Rieske [2Fe-2S] iron-sulfur domain profile.NDOB_PSEPU39-123  1A:39-123
NDOB_PSEU839-123  1A:39-123
2RING_HYDROXYL_ALPHAPS00570 Bacterial ring hydroxylating dioxygenases alpha-subunit signature.NDOB_PSEPU81-104  1A:81-104
NDOB_PSEU881-104  1A:81-104
Biological Unit 1 (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIESKEPS51296 Rieske [2Fe-2S] iron-sulfur domain profile.NDOB_PSEPU39-123  3A:39-123
NDOB_PSEU839-123  3A:39-123
2RING_HYDROXYL_ALPHAPS00570 Bacterial ring hydroxylating dioxygenases alpha-subunit signature.NDOB_PSEPU81-104  3A:81-104
NDOB_PSEU881-104  3A:81-104

(-) Exons   (0, 0)

(no "Exon" information available for 1O7W)

(-) 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:447
 aligned with NDOB_PSEPU | P0A110 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:447
                                    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       430       440       
           NDOB_PSEPU     1 MNYNNKILVSESGLSQKHLIHGDEELFQHELKTIFARNWLFLTHDSLIPAPGDYVTAKMGIDEVIVSRQNDGSIRAFLNVCRHRGKTLVSVEAGNAKGFVCSYHGWGFGSNGELQSVPFEKDLYGESLNKKCLGLKEVARVESFHGFIYGCFDQEAPPLMDYLGDAAWYLEPMFKHSGGLELVGPPGKVVIKANWKAPAENFVGDAYHVGWTHASSLRSGESIFSSLAGNAALPPEGAGLQMTSKYGSGMGVLWDGYSGVHSADLVPELMAFGGAKQERLNKEIGDVRARIYRSHLNCTVFPNNSMLTCSGVFKVWNPIDANTTEVWTYAIVEKDMPEDLKRRLADSVQRTFGPAGFWESDDNDNMETASQNGKKYQSRDSDLLSNLGFGEDVYGDAVYPGVVGKSAIGETSYRGFYRAYQAHVSSSNWAEFEHASSTWHTELTKTT 447
               SCOP domains d1o7wa1 A:1-154 Naphthalene 1,2-dioxygenase alpha subunit, N-domain                                                                                       d1o7wa2 A:155-447 Naphthalene 1,2-dioxygenase alpha subunit, C-domain                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1o7wA01 A:1-35,A:165-447           1o7wA02 A:36-164 'Rieske'-like iron-sulphur domains                                                                              1o7wA01 A:1-35,A:165-447 Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------Rieske-1o7wA02 A:38-139                                                                               -------------------Ring_hydroxyl_A-1o7wA01 A:159-426                                                                                                                                                                                                                                           --------------------- Pfam domains
         Sec.struct. author .........hhhh.eee.hhhhhhhhhhhhhhhh.....eeeee.hhh....eeeeeee..eeeeeee.....eeeee..............eee..eee......eee....eee..hhhhhh....hhhhh......eeeee..eeeee......hhhhhhhhhhhhhhhhhh....eeeeeeeeeeee...hhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhh.......eeeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...eeee....eeeeeeeee..eeeeeeeeeee...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh........eee........ee.......eee.....hhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) ---K-------F--T----------------R-----------------S-------------------S---------------------------------------------------E--------------------------------------------------I---------------------------------------------------A------V------------------------------------------S-------------------------------------------------------------------------------------------------------------------K-----------------------------R------------D------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                PROSITE (1) --------------------------------------RIESKE  PDB: A:39-123 UniProt: 39-123                                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------RING_HYDROXYL_ALPHA     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o7w A   1 MNYNNKILVSESGLSQKHLIHGDEELFQHELKTIFARNWLFLTHDSLIPAPGDYVTAKMGIDEVIVSRQNDGSIRAFLNVCRHRGKTLVSVEAGNAKGFVCSYHGWGFGSNGELQSVPFEKDLYGESLNKKCLGLKEVARVESFHGFIYGCFDQEAPPLMDYLGDAAWYLEPMFKHSGGLELVGPPGKVVIKANWKAPAENFVGDAYHVGWTHASSLRSGESIFSSLAGNAALPPEGAGLQMTSKYGSGMGVLWDGYSGVHSADLVPELMAFGGAKQERLNKEIGDVRARIYRSHLNCTVFPNNSMLTCSGVFKVWNPIDANTTEVWTYAIVEKDMPEDLKRRLADSVQRTFGPAGFWESDDNDNMETASQNGKKYQSRDSDLLSNLGFGEDVYGDAVYPGVVGKSAIGETSYRGFYRAYQAHVSSSNWAEFEHASSTWHTELTKTT 447
                                    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       430       440       

Chain A from PDB  Type:PROTEIN  Length:447
 aligned with NDOB_PSEU8 | P0A111 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:447
                                    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       430       440       
           NDOB_PSEU8     1 MNYNNKILVSESGLSQKHLIHGDEELFQHELKTIFARNWLFLTHDSLIPAPGDYVTAKMGIDEVIVSRQNDGSIRAFLNVCRHRGKTLVSVEAGNAKGFVCSYHGWGFGSNGELQSVPFEKDLYGESLNKKCLGLKEVARVESFHGFIYGCFDQEAPPLMDYLGDAAWYLEPMFKHSGGLELVGPPGKVVIKANWKAPAENFVGDAYHVGWTHASSLRSGESIFSSLAGNAALPPEGAGLQMTSKYGSGMGVLWDGYSGVHSADLVPELMAFGGAKQERLNKEIGDVRARIYRSHLNCTVFPNNSMLTCSGVFKVWNPIDANTTEVWTYAIVEKDMPEDLKRRLADSVQRTFGPAGFWESDDNDNMETASQNGKKYQSRDSDLLSNLGFGEDVYGDAVYPGVVGKSAIGETSYRGFYRAYQAHVSSSNWAEFEHASSTWHTELTKTT 447
               SCOP domains d1o7wa1 A:1-154 Naphthalene 1,2-dioxygenase alpha subunit, N-domain                                                                                       d1o7wa2 A:155-447 Naphthalene 1,2-dioxygenase alpha subunit, C-domain                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1o7wA01 A:1-35,A:165-447           1o7wA02 A:36-164 'Rieske'-like iron-sulphur domains                                                                              1o7wA01 A:1-35,A:165-447 Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------Rieske-1o7wA02 A:38-139                                                                               -------------------Ring_hydroxyl_A-1o7wA01 A:159-426                                                                                                                                                                                                                                           --------------------- Pfam domains
         Sec.struct. author .........hhhh.eee.hhhhhhhhhhhhhhhh.....eeeee.hhh....eeeeeee..eeeeeee.....eeeee..............eee..eee......eee....eee..hhhhhh....hhhhh......eeeee..eeeee......hhhhhhhhhhhhhhhhhh....eeeeeeeeeeee...hhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhh.......eeeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...eeee....eeeeeeeee..eeeeeeeeeee...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh........eee........ee.......eee.....hhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) ---K-------F--T----------------R-----------------S-------------------S---------------------------------------------------E--------------------------------------------------I---------------------------------------------------A------V------------------------------------------S-------------------------------------------------------------------------------------------------------------------K-----------------------------R------------D------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                PROSITE (2) --------------------------------------RIESKE  PDB: A:39-123 UniProt: 39-123                                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------RING_HYDROXYL_ALPHA     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o7w A   1 MNYNNKILVSESGLSQKHLIHGDEELFQHELKTIFARNWLFLTHDSLIPAPGDYVTAKMGIDEVIVSRQNDGSIRAFLNVCRHRGKTLVSVEAGNAKGFVCSYHGWGFGSNGELQSVPFEKDLYGESLNKKCLGLKEVARVESFHGFIYGCFDQEAPPLMDYLGDAAWYLEPMFKHSGGLELVGPPGKVVIKANWKAPAENFVGDAYHVGWTHASSLRSGESIFSSLAGNAALPPEGAGLQMTSKYGSGMGVLWDGYSGVHSADLVPELMAFGGAKQERLNKEIGDVRARIYRSHLNCTVFPNNSMLTCSGVFKVWNPIDANTTEVWTYAIVEKDMPEDLKRRLADSVQRTFGPAGFWESDDNDNMETASQNGKKYQSRDSDLLSNLGFGEDVYGDAVYPGVVGKSAIGETSYRGFYRAYQAHVSSSNWAEFEHASSTWHTELTKTT 447
                                    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       430       440       

Chain B from PDB  Type:PROTEIN  Length:193
 aligned with NDOC_PSEPU | P0A112 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191   
           NDOC_PSEPU     2 MINIQEDKLVSAHDAEEILRFFNCHDSALQQEATTLLTQEAHLLDIQAYRAWLEHCVGSEVQYQVISRELRAASERRYKLNEAMNVYNENFQQLKVRVEHQLDPQNWGNSPKLRFTRFITNVQAAMDVNDKELLHIRSNVILHRARRGNQVDVFYAAREDKWKRGEGGVRKLVQRFVDYPERILQTHNLMVFL 194
               SCOP domains d1o7wb_ B: Naphthalene 1,2-dioxygenase beta subunit                                                                                                                                               SCOP domains
               CATH domains 1o7wB00 B:502-694  [code=3.10.450.50, no name defined]                                                                                                                                            CATH domains
               Pfam domains --------------------------------------Ring_hydroxyl_B-1o7wB01 B:540-688                                                                                                                    ------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhheeeeeeeeeeee..............eeeeeeehhhhhhhhhhhhhh..hhhhh...eeeeeeeeeeeee......eeeeeeeeeeeeee...eeeeeeeeeeeeeee.hhh.eeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ---------------Q-F--------A----------------------------------------------------------------------I---------S-----------------R--D-E-------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o7w B 502 MINIQEDKLVSAHDAEEILRFFNCHDSALQQEATTLLTQEAHLLDIQAYRAWLEHCVGSEVQYQVISRELRAASERRYKLNEAMNVYNENFQQLKVRVEHQLDPQNWGNSPKLRFTRFITNVQAAMDVNDKELLHIRSNVILHRARRGNQVDVFYAAREDKWKRGEGGVRKLVQRFVDYPERILQTHNLMVFL 694
                                   511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691   

Chain B from PDB  Type:PROTEIN  Length:193
 aligned with NDOC_PSEU8 | P0A113 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191   
           NDOC_PSEU8     2 MINIQEDKLVSAHDAEEILRFFNCHDSALQQEATTLLTQEAHLLDIQAYRAWLEHCVGSEVQYQVISRELRAASERRYKLNEAMNVYNENFQQLKVRVEHQLDPQNWGNSPKLRFTRFITNVQAAMDVNDKELLHIRSNVILHRARRGNQVDVFYAAREDKWKRGEGGVRKLVQRFVDYPERILQTHNLMVFL 194
               SCOP domains d1o7wb_ B: Naphthalene 1,2-dioxygenase beta subunit                                                                                                                                               SCOP domains
               CATH domains 1o7wB00 B:502-694  [code=3.10.450.50, no name defined]                                                                                                                                            CATH domains
               Pfam domains --------------------------------------Ring_hydroxyl_B-1o7wB01 B:540-688                                                                                                                    ------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhheeeeeeeeeeee..............eeeeeeehhhhhhhhhhhhhh..hhhhh...eeeeeeeeeeeee......eeeeeeeeeeeeee...eeeeeeeeeeeeeee.hhh.eeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ---------------Q-F--------A----------------------------------------------------------------------I---------S-----------------R--D-E-------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o7w B 502 MINIQEDKLVSAHDAEEILRFFNCHDSALQQEATTLLTQEAHLLDIQAYRAWLEHCVGSEVQYQVISRELRAASERRYKLNEAMNVYNENFQQLKVRVEHQLDPQNWGNSPKLRFTRFITNVQAAMDVNDKELLHIRSNVILHRARRGNQVDVFYAAREDKWKRGEGGVRKLVQRFVDYPERILQTHNLMVFL 694
                                   511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691   

   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

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: NTF2 (66)

(-) Gene Ontology  (14, 40)

Asymmetric Unit(hide GO term definitions)
Chain A   (NDOB_PSEPU | P0A110)
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:0018625    naphthalene 1,2-dioxygenase activity    Catalysis of the reaction: naphthalene + NADH + H+ + O2 = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+.
    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 A   (NDOB_PSEU8 | P0A111)
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:0018625    naphthalene 1,2-dioxygenase activity    Catalysis of the reaction: naphthalene + NADH + H+ + O2 = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+.
    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.

Chain B   (NDOC_PSEU8 | P0A113)
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: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:0018625    naphthalene 1,2-dioxygenase activity    Catalysis of the reaction: naphthalene + NADH + H+ + O2 = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+.
    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.
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   (NDOC_PSEPU | P0A112)
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: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:0018625    naphthalene 1,2-dioxygenase activity    Catalysis of the reaction: naphthalene + NADH + H+ + O2 = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NDOB_PSEPU | P0A1101eg9 1ndo 1o7g 1o7h 1o7m 1o7n 1o7p 1uuv 1uuw
        NDOB_PSEU8 | P0A1111o7g 1o7h 1o7m 1o7n 1o7p 1uuv 2hmj 2hmk 2hml 2hmm 2hmn 2hmo 4hjl 4hkv 4hm0 4hm1 4hm2 4hm3 4hm4 4hm5 4hm6 4hm7 4hm8
        NDOC_PSEPU | P0A1121eg9 1ndo 1o7g 1o7h 1o7m 1o7n 1o7p 1uuv 1uuw
        NDOC_PSEU8 | P0A1131o7g 1o7h 1o7m 1o7n 1o7p 1uuv 2hmj 2hmk 2hml 2hmm 2hmn 2hmo 4hjl 4hkv 4hm0 4hm1 4hm2 4hm3 4hm4 4hm5 4hm6 4hm7 4hm8

(-) Related Entries Specified in the PDB File

1eg9 NAPHTHALENE 1,2-DIOXYGENASE WITH INDOLE BOUND IN THE ACTIVE SITE.
1ndo NAPTHALENE 1,2-DIOXYGENASE
1o7g NAPHTHALENE 1,2-DIOXYGENASE WITH NAPHTHALENE BOUND IN THE ACTIVE SITE.
1o7h NAPHTHALENE 1,2-DIOXYGENASE WITH OXIDIZED RIESKE IRON SULPHUR CENTER SITE.
1o7m NAPHTHALENE 1,2-DIOXYGENASE, BINARY COMPLEX WITH DIOXYGEN
1o7n NAPHTHALENE 1,2-DIOXYGENASE, TERNARY COMPLEX WITH DIOXYGEN AND INDOLE
1o7p NAPHTHALENE 1,2-DIOXYGENASE, PRODUCT COMPLEX