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(-) Description

Title :  CRYSTAL STRUCTURE OF DICAMBA MONOOXYGENASE
 
Authors :  M. A. Wilson, R. Dumitru, W. Z. Jiang, D. P. Weeks
Date :  10 Mar 09  (Deposition) - 21 Jul 09  (Release) - 22 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Rieske Cluster, Non-Heme Mononuclear Iron, Oxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Dumitru, W. Z. Jiang, D. P. Weeks, M. A. Wilson
Crystal Structure Of Dicamba Monooxygenase: A Rieske Nonheme Oxygenase That Catalyzes Oxidative Demethylation.
J. Mol. Biol. V. 392 498 2009
PubMed-ID: 19616011  |  Reference-DOI: 10.1016/J.JMB.2009.07.021
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DDMC
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DDMC
    Organism Common: PSEUDOMONAS MALTOPHILIA
    Organism Scientific: STENOTROPHOMONAS MALTOPHILIA
    Organism Taxid: 40324
    Strain: DI-6
    Synonym: DICAMBA MONOOXYGENASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric/Biological Unit (5, 19)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
3FE2Ligand/IonFE (III) ION
4FES3Ligand/IonFE2/S2 (INORGANIC) CLUSTER
5OXY1Ligand/IonOXYGEN MOLECULE

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:49 , HIS A:51 , ARG A:52 , CYS A:68 , TYR A:70 , HIS A:71 , GLY A:72 , LEU A:73BINDING SITE FOR RESIDUE FES A 500
02AC2SOFTWAREHIS A:160 , HIS A:165 , ASP A:294 , ACT A:354BINDING SITE FOR RESIDUE FE A 501
03AC3SOFTWARETRP A:9 , TYR A:10 , VAL A:11 , VAL A:225 , SER A:226 , ALA A:227 , ILE A:252 , LEU A:253 , THR A:254BINDING SITE FOR RESIDUE EDO A 350
04AC4SOFTWAREGLU A:16 , ARG A:130 , GLY A:139 , HOH A:464 , HOH A:487 , HOH A:516BINDING SITE FOR RESIDUE EDO A 351
05AC5SOFTWAREASP A:126 , GLY A:128 , CYS A:129 , LEU A:229 , ARG A:248 , HOH A:375 , HOH A:519BINDING SITE FOR RESIDUE EDO A 352
06AC6SOFTWAREASN A:230 , ILE A:232 , HIS A:251 , TRP A:285 , HOH A:359 , HOH A:428BINDING SITE FOR RESIDUE ACT A 353
07AC7SOFTWAREHIS A:160 , HIS A:165 , LEU A:290 , ASP A:294 , FE A:501 , HOH A:567BINDING SITE FOR RESIDUE ACT A 354
08AC8SOFTWARECYS B:49 , HIS B:51 , ARG B:52 , ALA B:54 , CYS B:68 , HIS B:71 , LEU B:73BINDING SITE FOR RESIDUE FES B 500
09AC9SOFTWAREASN B:154 , HIS B:160 , HIS B:165 , ASP B:294 , OXY B:600BINDING SITE FOR RESIDUE FE B 501
10BC1SOFTWAREHIS B:160 , HIS B:165 , ASP B:294 , FE B:501BINDING SITE FOR RESIDUE OXY B 600
11BC2SOFTWAREASN B:230 , ILE B:232 , HIS B:251 , TRP B:285 , HOH B:396BINDING SITE FOR RESIDUE ACT B 700
12BC3SOFTWARETRP B:9 , TYR B:10 , VAL B:11 , VAL B:225 , SER B:226 , ALA B:227 , ILE B:252 , LEU B:253 , THR B:254 , EDO B:351BINDING SITE FOR RESIDUE EDO B 350
13BC4SOFTWAREALA B:8 , TRP B:9 , PRO B:125 , LYS B:224 , VAL B:225 , EDO B:350 , HOH B:428BINDING SITE FOR RESIDUE EDO B 351
14BC5SOFTWAREMET B:156 , ASP B:157 , LEU B:158 , ARG B:179 , ALA B:190 , ASN B:218 , ILE B:220BINDING SITE FOR RESIDUE EDO B 352
15BC6SOFTWARECYS C:49 , HIS C:51 , ARG C:52 , CYS C:68 , TYR C:70 , HIS C:71 , LEU C:73BINDING SITE FOR RESIDUE FES C 500
16BC7SOFTWARETRP C:9 , TYR C:10 , VAL C:11 , LYS C:224 , VAL C:225 , SER C:226 , ALA C:227 , ILE C:252 , LEU C:253 , THR C:254 , HOH C:453 , HOH C:481BINDING SITE FOR RESIDUE EDO C 350
17BC8SOFTWAREGLU A:104 , HOH A:730 , HOH C:464BINDING SITE FOR RESIDUE EDO C 351
18BC9SOFTWAREGLU C:16 , ARG C:130 , VAL C:138 , GLY C:139 , HOH C:407 , HOH C:540BINDING SITE FOR RESIDUE EDO C 352
19CC1SOFTWAREALA B:117 , VAL C:62 , ASN C:63 , GLU C:74 , HOH C:376BINDING SITE FOR RESIDUE ACT C 353

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GKE)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Lys A:224 -Val A:225
2Lys B:224 -Val B:225
3Lys C:224 -Val C:225

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GKE)

(-) 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:340
 aligned with Q5S3I3_STEMA | Q5S3I3 from UniProtKB/TrEMBL  Length:339

    Alignment length:340
                                                                                                                                                                                                                                                                                                                                                                            339 
                                    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        |-
         Q5S3I3_STEMA     1 MTFVRNAWYVAALPEELSEKPLGRTILDTPLALYRQPDGVVAALLDICPHRFAPLSDGILVNGHLQCPYHGLEFDGGGQCVHNPHGNGARPASLNVRSFPVVERDALIWIWPGDPALADPGAIPDFGCRVDPAYRTVGGYGHVDCNYKLLVDNLMDLGHAQYVHRANAQTDAFDRLEREVIVGDGEIQALMKIPGGTPSVLMAKFLRGANTPVDAWNDIRWNKVSAMLNFIAVAPEGTPKEQSIHSRGTHILTPETEASCHYFFGSSRNFGIDDPEMDGVLRSWQAQALVKEDKVVVEAIERRRAYVEANGIRPAMLSCDEAAVRVSREIEKLEQLEAA-   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhh....eeeee..eeeeeee.....eeeee........hhhhheee..eee......ee.....eee........hhhhh.....eeee..eeee...hhhhhhhhhh..hhhhhh...eeeeeeeee..hhhhhhhhhhh..hhhhhhhhhhh..hhhhheeeeee...eeeeeeeeeee..hhhhhhhh......eeeeeeeeee...eeeeeeeeee...hhhhheeeeeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gke A   2 ATFVRNAWYVAALPEELSEKPLGRTILDTPLALYRQPDGVVAALLDICPHRFAPLSDGILVNGHLQCPYHGLEFDGGGQCVHNPHGNGARPASLNVRSFPVVERDALIWIWPGDPALADPGAIPDFGCRVDPAYRTVGGYGHVDCNYKLLVDNLMDLGHAQYVHRANAQTDAFDRLEREVIVGDGEIQALMKIPGGTPSVLMAKFLRGANTPVDAWNDIRWNKVSAMLNFIAVAPEGTPKEQSIHSRGTHILTPETEASCHYFFGSSRNFGIDDPEMDGVLRSWQAQALVKEDKVVVEAIERRRAYVEANGIRPAMLSCDEAAVRVSREIEKLEQLEAAR 341
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341


Chain B from PDB  Type:PROTEIN  Length:334
 aligned with Q5S3I3_STEMA | Q5S3I3 from UniProtKB/TrEMBL  Length:339

    Alignment length:340
                                                                                                                                                                                                                                                                                                                                                                            339 
                                    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        |-
         Q5S3I3_STEMA     1 MTFVRNAWYVAALPEELSEKPLGRTILDTPLALYRQPDGVVAALLDICPHRFAPLSDGILVNGHLQCPYHGLEFDGGGQCVHNPHGNGARPASLNVRSFPVVERDALIWIWPGDPALADPGAIPDFGCRVDPAYRTVGGYGHVDCNYKLLVDNLMDLGHAQYVHRANAQTDAFDRLEREVIVGDGEIQALMKIPGGTPSVLMAKFLRGANTPVDAWNDIRWNKVSAMLNFIAVAPEGTPKEQSIHSRGTHILTPETEASCHYFFGSSRNFGIDDPEMDGVLRSWQAQALVKEDKVVVEAIERRRAYVEANGIRPAMLSCDEAAVRVSREIEKLEQLEAA-   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhh....eeeee..eeeeeee.....eeeee........hhhhheee..eee......ee.....eee........hhhhh.....eeee..eeee...hhhhhhhhhh..hhhhhh...eeeeeeeee..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh...eeee..eeee..eeeee..hhhhhhh------.eeeeeeeeee...eeeeeeeeee...hhhhheeeeeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gke B   2 ATFVRNAWYVAALPEELSEKPLGRTILDTPLALYRQPDGVVAALLDICPHRFAPLSDGILVNGHLQCPYHGLEFDGGGQCVHNPHGNGARPASLNVRSFPVVERDALIWIWPGDPALADPGAIPDFGCRVDPAYRTVGGYGHVDCNYKLLVDNLMDLGHAQYVHRANAQTDAFDRLEREVIVGDGEIQALMKIPGGTPSVLMAKF------PVDAWNDIRWNKVSAMLNFIAVAPEGTPKEQSIHSRGTHILTPETEASCHYFFGSSRNFGIDDPEMDGVLRSWQAQALVKEDKVVVEAIERRRAYVEANGIRPAMLSCDEAAVRVSREIEKLEQLEAAR 341
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    |    - |     221       231       241       251       261       271       281       291       301       311       321       331       341
                                                                                                                                                                                                                                      206    213                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:314
 aligned with Q5S3I3_STEMA | Q5S3I3 from UniProtKB/TrEMBL  Length:339

    Alignment length:339
                                    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         
         Q5S3I3_STEMA     1 MTFVRNAWYVAALPEELSEKPLGRTILDTPLALYRQPDGVVAALLDICPHRFAPLSDGILVNGHLQCPYHGLEFDGGGQCVHNPHGNGARPASLNVRSFPVVERDALIWIWPGDPALADPGAIPDFGCRVDPAYRTVGGYGHVDCNYKLLVDNLMDLGHAQYVHRANAQTDAFDRLEREVIVGDGEIQALMKIPGGTPSVLMAKFLRGANTPVDAWNDIRWNKVSAMLNFIAVAPEGTPKEQSIHSRGTHILTPETEASCHYFFGSSRNFGIDDPEMDGVLRSWQAQALVKEDKVVVEAIERRRAYVEANGIRPAMLSCDEAAVRVSREIEKLEQLEAA 339
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhh....eeeee..eeeeeee.....eeeee........hhhhheee..eee......ee.....eee........hhhhh.....eeee..eeee...hhhhhhhhhh..hhhhhh...eeeeeeeee..hhhhhhhhhhh--------------------.eeeee...eeeeeeeee.......hhhhh-----.eeeeeeeeee...eeeeeeeeee...hhhhheeeeeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gke C   2 ATFVRNAWYVAALPEELSEKPLGRTILDTPLALYRQPDGVVAALLDICPHRFAPLSDGILVNGHLQCPYHGLEFDGGGQCVHNPHGNGARPASLNVRSFPVVERDALIWIWPGDPALADPGAIPDFGCRVDPAYRTVGGYGHVDCNYKLLVDNLMD--------------------EREVIVGDGEIQALMKIPGGTPSVLMAKFL-----PVDAWNDIRWNKVSAMLNFIAVAPEGTPKEQSIHSRGTHILTPETEASCHYFFGSSRNFGIDDPEMDGVLRSWQAQALVKEDKVVVEAIERRRAYVEANGIRPAMLSCDEAAVRVSREIEKLEQLEAA 340
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151     |   -         -      |181       191       201     |   - |     221       231       241       251       261       271       281       291       301       311       321       331         
                                                                                                                                                                                     157                  178                          207   213
   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  (0, 0)

(no "SCOP Domain" information available for 3GKE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q5S3I3_STEMA | Q5S3I3)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO: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: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)

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        Q5S3I3_STEMA | Q5S3I3: 3gb4 3gl0 3gl2 3gob 3gte 3gts

(-) Related Entries Specified in the PDB File

3gl0 3gl2