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(-) Description

Title :  NAPHTHALENE 1,2-DIOXYGENASE BOUND TO INDOLE-3-ACETATE
 
Authors :  D. J. Ferraro, S. Ramaswamy
Date :  17 Oct 12  (Deposition) - 30 Oct 13  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Ferraro, S. Ramaswamy
Naphthalene 1, 2-Dioxygenase Bound To Indole-3-Acetate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NAPHTHALENE 1,2-DIOXYGENASE SUBUNIT ALPHA
    Chains: A
    EC Number: 1.14.12.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDTG121
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DOXB, NC_004999.1
    Organism Scientific: PSEUDOMONAS SP. C18
    Organism Taxid: 69011
    Strain: NCIB 9816-4
    Synonym: NAPHTHALENE 1,2-DIOXYGENASE ISP ALPHA
 
Molecule 2 - NAPHTHALENE 1,2-DIOXYGENASE SUBUNIT BETA
    Chains: B
    EC Number: 1.14.12.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDTG121
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DOXD, NC_004999.1
    Organism Scientific: PSEUDOMONAS SP. C18
    Organism Taxid: 69011
    Strain: NCIB 9816-4
    Synonym: NAPHTHALENE 1,2-DIOXYGENASE ISP BETA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 23)

Asymmetric Unit (5, 23)
No.NameCountTypeFull Name
1EDO15Ligand/Ion1,2-ETHANEDIOL
2FE1Ligand/IonFE (III) ION
3FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
4IAC1Ligand/Ion1H-INDOL-3-YLACETIC ACID
5SO45Ligand/IonSULFATE ION
Biological Unit 1 (4, 66)
No.NameCountTypeFull Name
1EDO45Ligand/Ion1,2-ETHANEDIOL
2FE-1Ligand/IonFE (III) ION
3FES3Ligand/IonFE2/S2 (INORGANIC) CLUSTER
4IAC3Ligand/Ion1H-INDOL-3-YLACETIC ACID
5SO415Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:31 , PHE A:35 , ALA A:36 , 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 A 501
02AC2SOFTWAREHIS A:18 , CYS A:81 , ARG A:82 , SER A:381 , ASP A:382 , LEU A:383 , HOH A:783 , HOH A:807 , HOH A:808BINDING SITE FOR RESIDUE EDO A 502
03AC3SOFTWAREGLU A:24 , LYS A:374 , HOH A:809 , HOH A:810BINDING SITE FOR RESIDUE EDO A 503
04AC4SOFTWAREHIS A:208 , HIS A:213 , ASP A:362 , IAC A:505BINDING SITE FOR RESIDUE FE A 504
05AC5SOFTWAREASN A:201 , ASP A:205 , HIS A:208 , HIS A:213 , HIS A:295 , ASN A:297 , PHE A:352 , ASP A:362 , FE A:504BINDING SITE FOR RESIDUE IAC A 505
06AC6SOFTWARETRP A:439 , HOH A:671 , HOH A:712BINDING SITE FOR RESIDUE SO4 A 506
07AC7SOFTWARELEU A:128 , ASN A:129 , LYS A:130 , LYS A:131BINDING SITE FOR RESIDUE SO4 A 507
08AC8SOFTWARECYS A:81 , HIS A:83 , ARG A:84 , CYS A:101 , HIS A:104 , TRP A:106BINDING SITE FOR RESIDUE FES A 508
09AC9SOFTWAREVAL A:183 , ARG A:342 , ASP A:346 , HOH A:724BINDING SITE FOR RESIDUE EDO A 509
10BC1SOFTWARETHR A:56 , GLU A:92 , PRO A:186 , LYS A:188 , TRP A:327 , GLU B:570 , ARG B:683BINDING SITE FOR RESIDUE EDO A 510
11BC2SOFTWAREASP A:361 , ASP A:364 , HOH A:603 , HOH A:816 , HOH A:857 , TRP B:608 , GLY B:609 , ARG B:648BINDING SITE FOR RESIDUE EDO A 511
12BC3SOFTWAREGLU A:142 , SER A:143 , EDO A:513BINDING SITE FOR RESIDUE EDO A 512
13BC4SOFTWARESER A:73 , ILE A:74 , SER A:143 , EDO A:512 , HOH A:874BINDING SITE FOR RESIDUE EDO A 513
14BC5SOFTWAREASP A:396 , ALA A:397 , VAL A:398 , PRO A:400 , HIS A:440 , HOH A:716 , HOH A:811BINDING SITE FOR RESIDUE EDO A 514
15BC6SOFTWAREPRO A:337 , GLU A:338 , HOH A:688BINDING SITE FOR RESIDUE SO4 A 515
16BC7SOFTWAREASP B:546 , ARG B:615 , PHE B:616 , EDO B:705 , HOH B:851BINDING SITE FOR RESIDUE EDO B 701
17BC8SOFTWAREGLY B:559 , SER B:560 , GLY B:666 , GLU B:667 , LYS B:672 , HOH B:914BINDING SITE FOR RESIDUE SO4 B 702
18BC9SOFTWARETYR B:588 , MET B:691 , VAL B:692 , PHE B:693 , HOH B:841 , HOH B:884BINDING SITE FOR RESIDUE EDO B 703
19CC1SOFTWAREASN B:591 , GLN B:594 , HOH B:840 , HOH B:904BINDING SITE FOR RESIDUE EDO B 704
20CC2SOFTWAREARG B:638 , ALA B:658 , GLU B:660 , VAL B:678 , ASP B:679 , EDO B:701 , HOH B:868BINDING SITE FOR RESIDUE EDO B 705
21CC3SOFTWAREVAL A:190 , GLN B:686 , THR B:687 , HIS B:688BINDING SITE FOR RESIDUE EDO B 706
22CC4SOFTWARETHR B:535 , THR B:539 , ILE B:620 , THR B:621 , ASN B:622BINDING SITE FOR RESIDUE EDO B 707
23CC5SOFTWARELYS B:632 , ARG B:665 , GLY B:669 , ARG B:671 , HOH B:899BINDING SITE FOR RESIDUE SO4 B 708

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HM0)

(-) 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  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HM0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HM0)

(-) Exons   (0, 0)

(no "Exon" information available for 4HM0)

(-) 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:448
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4hm0a1 A:1-154 Naphthalene 1,2-dioxygenase alpha subunit, N-domain                                                                                       d4hm0a2 A:155-448 Naphthalene 1,2-dioxygenase alpha subunit, C-domain                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhh.eee.hhhhhhhhhhhhhhhh.....eeeee........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.hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hm0 A   1 MNYNNKILVSESGLSQKHLIHGDEELFQHELKTIFARNWLFLTHDSLIPAPGDYVTAKMGIDEVIVSRQNDGSIRAFLNVCRHRGKTLVSVEAGNAKGFVCSYHGWGFGSNGELQSVPFEKDLYGESLNKKCLGLKEVARVESFHGFIYGCFDQEAPPLMDYLGDAAWYLEPMFKHSGGLELVGPPGKVVIKANWKAPAENFVGDAYHVGWTHASSLRSGESIFSSLAGNAALPPEGAGLQMTSKYGSGMGVLWDGYSGVHSADLVPELMAFGGAKQERLNKEIGDVRARIYRSHLNCTVFPNNSMLTCSGVFKVWNPIDANTTEVWTYAIVEKDMPEDLKRRLADSVQRTFGPAGFWESDDNDNMETASQNGKKYQSRDSDLLSNLGFGEDVYGDAVYPGVVGKSAIGETSYRGFYRAYQAHVSSSNWAEFEHASSTWHTELTKTTD 448
                                    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
                                                                                                                                                                                                                                 
               SCOP domains d4hm0b_ B: Naphthalene 1,2-dioxygenase beta subunit                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhheeeeeeeeeeee..............eeeeeeehhhhhhhhhhhhhh..hhhhh...eeeeeeeeeeeee......eeeeeeeeeeeeee...eeeeeeeeeeeeeee.hhh.eeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hm0 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
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HM0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HM0)

(-) Gene Ontology  (13, 19)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NDOB_PSEU8 | P0A111: 1o7g 1o7h 1o7m 1o7n 1o7p 1o7w 1uuv 2hmj 2hmk 2hml 2hmm 2hmn 2hmo 4hjl 4hkv 4hm1 4hm2 4hm3 4hm4 4hm5 4hm6 4hm7 4hm8
        NDOC_PSEU8 | P0A113: 1o7g 1o7h 1o7m 1o7n 1o7p 1o7w 1uuv 2hmj 2hmk 2hml 2hmm 2hmn 2hmo 4hjl 4hkv 4hm1 4hm2 4hm3 4hm4 4hm5 4hm6 4hm7 4hm8

(-) Related Entries Specified in the PDB File

4hm1 4hm2 4hm3 4hm4 4hm5 4hm6 4hm7 4hm8