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(-) Description

Title :  NAPTHALENE 1,2-DIOXYGENASE
 
Authors :  S. Ramaswamy, B. Kauppi, E. Carredano
Date :  11 Jan 98  (Deposition) - 23 Mar 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Non-Heme Iron Dioxygenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Kauppi, K. Lee, E. Carredano, R. E. Parales, D. T. Gibson, H. Eklund, S. Ramaswamy
Structure Of An Aromatic-Ring-Hydroxylating Dioxygenase-Naphthalene 1, 2-Dioxygenase.
Structure V. 6 571 1998
PubMed-ID: 9634695  |  Reference-DOI: 10.1016/S0969-2126(98)00059-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NAPTHALENE 1,2-DIOXYGENASE
    Chains: A, C, E
    Collection: NCIB 9816
    EC Number: 1.14.12.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: NAHACAD
    Expression System Plasmid: PDTG141
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Variant: DE3
    Gene: NAHACAD
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Other Details: CHAIN A,C,E AND B,D,F ARE THE LARGE AND THE SMALL SUBUNITS RESPECTIVELY
 
Molecule 2 - NAPTHALENE 1,2-DIOXYGENASE
    Chains: B, D, F
    Collection: NCIB 9816
    EC Number: 1.14.12.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: NAHACAD
    Expression System Plasmid: PDTG141
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Variant: DE3
    Gene: NAHACAD
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Other Details: CHAIN A,C,E AND B,D,F ARE THE LARGE AND THE SMALL SUBUNITS RESPECTIVELY

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1FE3Ligand/IonFE (III) ION
2FES3Ligand/IonFE2/S2 (INORGANIC) CLUSTER

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:208 , HIS A:213 , ASP A:362BINDING SITE FOR RESIDUE FE A 452
02AC2SOFTWAREASN C:201 , HIS C:208 , HIS C:213 , ASP C:362BINDING SITE FOR RESIDUE FE C 452
03AC3SOFTWAREHIS E:208 , HIS E:213 , ASP E:362BINDING SITE FOR RESIDUE FE E 452
04AC4SOFTWARECYS A:81 , HIS A:83 , ARG A:84 , CYS A:101 , TYR A:103 , HIS A:104 , TRP A:106BINDING SITE FOR RESIDUE FES A 451
05AC5SOFTWARECYS C:81 , HIS C:83 , ARG C:84 , CYS C:101 , TYR C:103 , HIS C:104 , TRP C:106BINDING SITE FOR RESIDUE FES C 451
06AC6SOFTWARECYS E:81 , HIS E:83 , ARG E:84 , CYS E:101 , TYR E:103 , HIS E:104 , TRP E:106BINDING SITE FOR RESIDUE FES E 451
07MO1UNKNOWNHIS A:213 , HIS A:208 , ASP A:362MONO IRON SITE - THERE IS ALSO A WATER.
08MO2UNKNOWNHIS C:213 , HIS C:208 , ASP C:362MONO IRON SITE - THERE IS ALSO A WATER.
09MO3UNKNOWNHIS E:213 , HIS E:208 , ASP E:362MONO IRON SITE - THERE IS ALSO A WATER.
10RK1UNKNOWNCYS A:81 , CYS A:101 , HIS A:83 , HIS C:104RIESKE CENTER - FIRST TWO ARE LIGANDS TO FE1 AND THE NEXT TO FE2.
11RK2UNKNOWNCYS C:81 , CYS C:101 , HIS C:83 , HIS C:104RIESKE CENTER - FIRST TWO ARE LIGANDS TO FE1 AND THE NEXT TO FE2.
12RK3UNKNOWNCYS E:81 , CYS E:101 , HIS E:83 , HIS E:104RIESKE CENTER - FIRST TWO ARE LIGANDS TO FE1 AND THE NEXT TO FE2.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Gly A:184 -Pro A:185
2Phe A:301 -Pro A:302
3Ser B:611 -Pro B:612
4Gly C:184 -Pro C:185
5Phe C:301 -Pro C:302
6Ser D:611 -Pro D:612
7Gly E:184 -Pro E:185
8Phe E:301 -Pro E:302
9Ser F:611 -Pro F:612

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (23, 69)

Asymmetric/Biological Unit (23, 69)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_NDOB_PSEPU_001 *N4KNDOB_PSEPU  ---  ---A/C/EN4K
02UniProtVAR_NDOB_PSEPU_002 *S12FNDOB_PSEPU  ---  ---A/C/ES12F
03UniProtVAR_NDOB_PSEPU_003 *S15TNDOB_PSEPU  ---  ---A/C/ES15T
04UniProtVAR_NDOB_PSEPU_004 *K32RNDOB_PSEPU  ---  ---A/C/EK32R
05UniProtVAR_NDOB_PSEPU_005 *A50SNDOB_PSEPU  ---  ---A/C/EA50S
06UniProtVAR_NDOB_PSEPU_006 *N70SNDOB_PSEPU  ---  ---A/C/EN70S
07UniProtVAR_NDOB_PSEPU_007 *D122ENDOB_PSEPU  ---  ---A/C/ED122E
08UniProtVAR_NDOB_PSEPU_008 *M173INDOB_PSEPU  ---  ---A/C/EM173I
09UniProtVAR_NDOB_PSEPU_009 *S225ANDOB_PSEPU  ---  ---A/C/ES225A
10UniProtVAR_NDOB_PSEPU_010 *S225CNDOB_PSEPU  ---  ---A/C/ES225C
11UniProtVAR_NDOB_PSEPU_011 *A232VNDOB_PSEPU  ---  ---A/C/EA232V
12UniProtVAR_NDOB_PSEPU_012 *A275SNDOB_PSEPU  ---  ---A/C/EA275S
13UniProtVAR_NDOB_PSEPU_013 *E391KNDOB_PSEPU  ---  ---A/C/EE391K
14UniProtVAR_NDOB_PSEPU_014 *Q421RNDOB_PSEPU  ---  ---A/C/EQ421R
15UniProtVAR_NDOB_PSEPU_015 *H434DNDOB_PSEPU  ---  ---A/C/EH434D
16UniProtVAR_NDOC_PSEPU_001 *E17QNDOC_PSEPU  ---  ---B/D/FE517Q
17UniProtVAR_NDOC_PSEPU_002 *I19FNDOC_PSEPU  ---  ---B/D/FI519F
18UniProtVAR_NDOC_PSEPU_003 *S28ANDOC_PSEPU  ---  ---B/D/FS528A
19UniProtVAR_NDOC_PSEPU_004 *V99INDOC_PSEPU  ---  ---B/D/FV599I
20UniProtVAR_NDOC_PSEPU_005 *G109SNDOC_PSEPU  ---  ---B/D/FG609S
21UniProtVAR_NDOC_PSEPU_006 *M127RNDOC_PSEPU  ---  ---B/D/FM627R
22UniProtVAR_NDOC_PSEPU_007 *N130DNDOC_PSEPU  ---  ---B/D/FN630D
23UniProtVAR_NDOC_PSEPU_008 *K132ENDOC_PSEPU  ---  ---B/D/FK632E
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 6)

Asymmetric/Biological Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIESKEPS51296 Rieske [2Fe-2S] iron-sulfur domain profile.NDOB_PSEPU39-123
 
 		  3A:39-123
C:39-123
E:39-123
2RING_HYDROXYL_ALPHAPS00570 Bacterial ring hydroxylating dioxygenases alpha-subunit signature.NDOB_PSEPU81-104
 
 		  3A:81-104
C:81-104
E:81-104

(-) Exons   (0, 0)

(no "Exon" information available for 1NDO)

(-) 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: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 d1ndoa1 A:1-154 Naphthalene 1,2-dioxygenase alpha subunit, N-domain                                                                                       d1ndoa2 A:155-447 Naphthalene 1,2-dioxygenase alpha subunit, C-domain                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1ndoA01 A:1-35,A:165-447           1ndoA02 A:36-164 'Rieske'-like iron-sulphur domains                                                                              1ndoA01 A:1-35,A:165-447 Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhh.eeehhhh..hhhhhhhhhh......eeeeehhh.....eeeeeee..eeeeeee.....eeeee..............eee..eee......eee..........hhhh......hhh.......eeeee..eeeee.......hhhhhhhhhhhhhhhh.....eeee...eeeee...hhhhhhhhhh....hhhh.hhhhhhh....hhhhhh........eeeee.....eeeee.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.eeeeee...eeee....eeeeeeeee..eeeeeeeeeee....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......eee.................eee......hhhhhhhhhhhhhh....hhhhhhhh..hhhhh.... 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) --------------------------------------------------------------------------------RING_HYDROXYL_ALPHA     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ndo 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 d1ndob_ B: Naphthalene 1,2-dioxygenase beta subunit                                                                                                                                               SCOP domains
               CATH domains 1ndoB00 B:502-694  [code=3.10.450.50, no name defined]                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhhhhh.....eeeeeee..............eeeeeee.hhhhhhhhhhhh....hhh....eeeeeee..eeee......eeeeeeeeeeeeee...eeeeeeeeeeeeeee.....eeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ---------------Q-F--------A----------------------------------------------------------------------I---------S-----------------R--D-E-------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ndo B 502 MINIQEDKLVSAHDAEEILRFFNCHDSALQQEATTLLTQEAHLLDIQAYRAWLEHCVGSEVQYQVISRELRAASERRYKLNEAMNVYNENFQQLKVRVEHQLDPQNWGNSPKLRFTRFITNVQAAMDVNDKELLHIRSNVILHRARRGNQVDVFYAAREDKWKRGEGGVRKLVQRFVDYPERILQTHNLMVFL 694
                                   511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691   


Chain C 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 d1ndoc1 C:1-154 Naphthalene 1,2-dioxygenase alpha subunit, N-domain                                                                                       d1ndoc2 C:155-447 Naphthalene 1,2-dioxygenase alpha subunit, C-domain                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1ndoC01 C:1-35,C:165-447           1ndoC02 C:36-164 'Rieske'-like iron-sulphur domains                                                                              1ndoC01 C:1-35,C:165-447 Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhh.eeehhhh..hhhhhhhhhh......eeeeehhh.....eeeeeee..eeeeeee.....eeeee..............eee..eee......eee..........hhhh......hhh.......eeeee..eeeee.......hhhhhhhhhhhhhhhh.....eeee...eeeee...hhhhhhhhhh....hhhh.hhhhhhh....hhhhhh........eeeee.....eeeee.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.eeeeee...eeee....eeeeeeeee..eeeeeeeeeee....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhh..eee.................eee......hhhhhhhhhhhhhh....hhhhhhhh..hhhhhh... 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: C:39-123 UniProt: 39-123                                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------RING_HYDROXYL_ALPHA     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ndo C   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 D 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 d1ndod_ D: Naphthalene 1,2-dioxygenase beta subunit                                                                                                                                               SCOP domains
               CATH domains 1ndoD00 D:502-694  [code=3.10.450.50, no name defined]                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhhhhh.....eeeeeee..............eeeeeee.hhhhhhhhhhhh....hhh....eeeeeee..eeee......eeeeeeeeeeeeee...eeeeeeeeeeeeeee.hhh.eeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ---------------Q-F--------A----------------------------------------------------------------------I---------S-----------------R--D-E-------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ndo D 502 MINIQEDKLVSAHDAEEILRFFNCHDSALQQEATTLLTQEAHLLDIQAYRAWLEHCVGSEVQYQVISRELRAASERRYKLNEAMNVYNENFQQLKVRVEHQLDPQNWGNSPKLRFTRFITNVQAAMDVNDKELLHIRSNVILHRARRGNQVDVFYAAREDKWKRGEGGVRKLVQRFVDYPERILQTHNLMVFL 694
                                   511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691   


Chain E from PDB  Type:PROTEIN  Length:445
 aligned with NDOB_PSEPU | P0A110 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:445
                                    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 MNYNNKILVSESGLSQKHLIHGDEELFQHELKTIFARNWLFLTHDSLIPAPGDYVTAKMGIDEVIVSRQNDGSIRAFLNVCRHRGKTLVSVEAGNAKGFVCSYHGWGFGSNGELQSVPFEKDLYGESLNKKCLGLKEVARVESFHGFIYGCFDQEAPPLMDYLGDAAWYLEPMFKHSGGLELVGPPGKVVIKANWKAPAENFVGDAYHVGWTHASSLRSGESIFSSLAGNAALPPEGAGLQMTSKYGSGMGVLWDGYSGVHSADLVPELMAFGGAKQERLNKEIGDVRARIYRSHLNCTVFPNNSMLTCSGVFKVWNPIDANTTEVWTYAIVEKDMPEDLKRRLADSVQRTFGPAGFWESDDNDNMETASQNGKKYQSRDSDLLSNLGFGEDVYGDAVYPGVVGKSAIGETSYRGFYRAYQAHVSSSNWAEFEHASSTWHTELTK 445
               SCOP domains d1ndoe1 E:1-154 Naphthalene 1,2-dioxygenase alpha subunit, N-domain                                                                                       d1ndoe2 E:155-445 Naphthalene 1,2-dioxygenase alpha subunit, C-domain                                                                                                                                                                                                                               SCOP domains
               CATH domains 1ndoE01 E:1-35,E:165-445           1ndoE02 E:36-164 'Rieske'-like iron-sulphur domains                                                                              1ndoE01 E:1-35,E:165-445 Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1                                                                                                                                                                                                     CATH domains
           Pfam domains (1) -------------------------------------Rieske-1ndoE04 E:38-139                                                                               -------------------Ring_hydroxyl_A-1ndoE01 E:159-426                                                                                                                                                                                                                                           ------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------Rieske-1ndoE05 E:38-139                                                                               -------------------Ring_hydroxyl_A-1ndoE02 E:159-426                                                                                                                                                                                                                                           ------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------Rieske-1ndoE06 E:38-139                                                                               -------------------Ring_hydroxyl_A-1ndoE03 E:159-426                                                                                                                                                                                                                                           ------------------- Pfam domains (3)
         Sec.struct. author ..........hhh.eeehhhh..hhhhhhhhhh......eeeee........eeeeeee..eeeeeee.....eeeee..............eee..eee......eee..........hhhh......hhh.......eeeee..eeeee.......hhhhhhhhhhhhhhhh.....eeee...eeeee...hhhhhhhhhh....hhhh.hhhhhhh....hhhhhh........eeeee.....eeeee.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.eeeeee...eeee....eeeeeeeee..eeeeeeeeeee....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......eee.................eee......hhhhhhhhhhhhhh....hhhhhhhh..hhhhh.. 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: E:39-123 UniProt: 39-123                                                ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------RING_HYDROXYL_ALPHA     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ndo E   1 MNYNNKILVSESGLSQKHLIHGDEELFQHELKTIFARNWLFLTHDSLIPAPGDYVTAKMGIDEVIVSRQNDGSIRAFLNVCRHRGKTLVSVEAGNAKGFVCSYHGWGFGSNGELQSVPFEKDLYGESLNKKCLGLKEVARVESFHGFIYGCFDQEAPPLMDYLGDAAWYLEPMFKHSGGLELVGPPGKVVIKANWKAPAENFVGDAYHVGWTHASSLRSGESIFSSLAGNAALPPEGAGLQMTSKYGSGMGVLWDGYSGVHSADLVPELMAFGGAKQERLNKEIGDVRARIYRSHLNCTVFPNNSMLTCSGVFKVWNPIDANTTEVWTYAIVEKDMPEDLKRRLADSVQRTFGPAGFWESDDNDNMETASQNGKKYQSRDSDLLSNLGFGEDVYGDAVYPGVVGKSAIGETSYRGFYRAYQAHVSSSNWAEFEHASSTWHTELTK 445
                                    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 F 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 d1ndof_ F: Naphthalene 1,2-dioxygenase beta subunit                                                                                                                                               SCOP domains
               CATH domains 1ndoF00 F:502-694  [code=3.10.450.50, no name defined]                                                                                                                                            CATH domains
           Pfam domains (1) --------------------------------------Ring_hydroxyl_B-1ndoF01 F:540-688                                                                                                                    ------ Pfam domains (1)
           Pfam domains (2) --------------------------------------Ring_hydroxyl_B-1ndoF02 F:540-688                                                                                                                    ------ Pfam domains (2)
           Pfam domains (3) --------------------------------------Ring_hydroxyl_B-1ndoF03 F:540-688                                                                                                                    ------ Pfam domains (3)
         Sec.struct. author ...........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhhhhh.....eeeeeee..............eeeeeee.hhhhhhhhhhhh....hhh....eeeeeee..eeee......eeeeeeeeeeeeee...eeeeeeeeeeeeeee.hhh.eeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ---------------Q-F--------A----------------------------------------------------------------------I---------S-----------------R--D-E-------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ndo F 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, 9)

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

(-) CATH Domains  (3, 9)

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

(-) Pfam Domains  (3, 9)

Asymmetric/Biological Unit
(-)
Clan: Bet_V_1_like (93)
(-)
Clan: ISP-domain (54)
(-)
Clan: NTF2 (66)

(-) Gene Ontology  (14, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C,E   (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 B,D,F   (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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  1.14.12.12
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 Related Entries

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

UniProtKB/Swiss-Prot
        NDOB_PSEPU | P0A110: 1eg9 1o7g 1o7h 1o7m 1o7n 1o7p 1o7w 1uuv 1uuw
        NDOC_PSEPU | P0A112: 1eg9 1o7g 1o7h 1o7m 1o7n 1o7p 1o7w 1uuv 1uuw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1NDO)