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(-) Description

Title :  1.20 A RESOLUTION CRYSTAL STRUCTURE OF DIOXYGEN BOUND COPPER-CONTAINING NITRITE REDUCTASE FROM GEOBACILLUS THERMODENITRIFICANS
 
Authors :  Y. Fukuda, T. Inoue
Date :  10 Dec 13  (Deposition) - 10 Dec 14  (Release) - 10 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Greek Key Beta Barrel, Dissimilatory Nitrite Reductase, Periplasm- Like Space, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Fukuda, T. Inoue
Crystallographic Evidence For Side-On Dioxygen Trapped On Type 2 Copper In Copper-Containing Nitrite Reductase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NITRITE REDUCTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 31-352
    Gene: NIRK
    Organism Scientific: GEOBACILLUS THERMODENITRIFICANS
    Organism Taxid: 420246
    Strain: NG80-2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 18)

Asymmetric Unit (7, 18)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID
2CU6Ligand/IonCOPPER (II) ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
4MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NA1Ligand/IonSODIUM ION
6OXY1Ligand/IonOXYGEN MOLECULE
7SO43Ligand/IonSULFATE ION
Biological Unit 1 (5, 33)
No.NameCountTypeFull Name
1ACY12Ligand/IonACETIC ACID
2CU-1Ligand/IonCOPPER (II) ION
3EDO6Ligand/Ion1,2-ETHANEDIOL
4MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NA-1Ligand/IonSODIUM ION
6OXY3Ligand/IonOXYGEN MOLECULE
7SO49Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:95 , CYS A:135 , HIS A:143 , MET A:148BINDING SITE FOR RESIDUE CU A 401
02AC2SOFTWAREHIS A:100 , HIS A:134 , HIS A:294 , OXY A:408 , HOH A:821 , HOH A:856BINDING SITE FOR RESIDUE CU A 402
03AC3SOFTWAREHIS A:42 , GLU A:53 , HIS A:83 , HOH A:704 , HOH A:800BINDING SITE FOR RESIDUE CU A 403
04AC4SOFTWAREHIS A:39BINDING SITE FOR RESIDUE CU A 404
05AC5SOFTWAREGLU A:239 , HOH A:628 , HOH A:770 , HOH A:813 , HOH A:814 , HOH A:853BINDING SITE FOR RESIDUE CU A 405
06AC6SOFTWAREASP A:167 , HOH A:693 , HOH A:741 , HOH A:806 , HOH A:843BINDING SITE FOR RESIDUE CU A 406
07AC7SOFTWAREASP A:40 , HOH A:815 , HOH A:835BINDING SITE FOR RESIDUE NA A 407
08AC8SOFTWAREASP A:98 , HIS A:100 , HIS A:134 , HIS A:244 , VAL A:246 , HIS A:294 , PHE A:296 , CU A:402 , HOH A:783 , HOH A:821 , HOH A:856BINDING SITE FOR RESIDUE OXY A 408
09AC9SOFTWAREASP A:163 , VAL A:166 , ASP A:167 , ARG A:168 , GLU A:169 , ARG A:229 , HOH A:719 , HOH A:803BINDING SITE FOR RESIDUE MPD A 409
10BC1SOFTWARELYS A:138 , PRO A:139 , GLN A:300 , HOH A:560BINDING SITE FOR RESIDUE EDO A 410
11BC2SOFTWAREASN A:158 , GLY A:159 , TYR A:160 , ASP A:163 , LYS A:164 , HOH A:724 , HOH A:778BINDING SITE FOR RESIDUE EDO A 411
12BC3SOFTWAREHIS A:262 , LEU A:263 , HOH A:750BINDING SITE FOR RESIDUE SO4 A 412
13BC4SOFTWAREMET A:270 , HOH A:850BINDING SITE FOR RESIDUE SO4 A 413
14BC5SOFTWARELYS A:22 , GLY A:23 , LYS A:61 , HOH A:683 , HOH A:852BINDING SITE FOR RESIDUE SO4 A 414
15BC6SOFTWAREPRO A:290 , HOH A:716 , HOH A:783 , HOH A:857BINDING SITE FOR RESIDUE ACY A 415
16BC7SOFTWAREASP A:55 , LYS A:56 , THR A:212 , PHE A:213 , HOH A:583BINDING SITE FOR RESIDUE ACY A 416
17BC8SOFTWARELYS A:127 , PRO A:128 , ASN A:258 , ASN A:260 , HOH A:572 , HOH A:754 , HOH A:804 , HOH A:805BINDING SITE FOR RESIDUE ACY A 417
18BC9SOFTWAREARG A:168 , LYS A:223 , THR A:312 , GLU A:314 , HOH A:840 , HOH A:841BINDING SITE FOR RESIDUE ACY A 418

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ala A:69 -Pro A:70
2Lys A:138 -Pro A:139
3Gly A:236 -Pro A:237

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WNJ)

(-) 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:298
 aligned with A4IL26_GEOTN | A4IL26 from UniProtKB/TrEMBL  Length:352

    Alignment length:298
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336        
         A4IL26_GEOTN    47 IAAHKGVNQAPVPLKMERVGPHDVHIEMTAQITDIEIDKGKIYKAWTFNGQAPGPLVVVNEGDTIHFTLKNMDPVVPHSMDFHAVHASPSKDFIDVMPNKSGTFTYPANKPGVFMYHCGTKPVLQHIANGMHGVIIVKPKNGYPTDKEVDREYVLIQNEWYKYNDMNDFQNGVPSYVVFSSKALKPGDPNTNGDTFTLKEKPLLAKVGEKIRLYINNVGPNEVSSFHVVGTVFDDVYLDGNPNNHLQGMQTVMLPASGGAVVEFTVTRPGTYPIVTHQFNHAQKGAVAMLKVTETGED 344
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.........eeeeee..eeeeeeeeeeeeeeee..eeeeeeee........eeee..eeeeeeeee.........ee.....hhhhhh.......eeeeeeee...eeeeee....hhhhhhhh..eeeeeee......hhhhh.eeeeeeeeee....hhhhhhhh...eeeeee..............hhhhhh.eeee...eeeeeeeeee....eeeee....eeeeee......eeeee..eee....eeeeeee....eeeeeee.hhhhhhh..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wnj A  18 IAAHKGVNQAPVPLKMERVGPHDVHIEMTAQITDIEIDKGKIYKAWTFNGQAPGPLVVVNEGDTIHFTLKNMDPVVPHSMDFHAVHASPSKDFIDVMPNKSGTFTYPANKPGVFMYHCGTKPVLQHIANGMHGVIIVKPKNGYPTDKEVDREYVLIQNEWYKYNDMNDFQNGVPSYVVFSSKALKPGDPNTNGDTFTLKEKPLLAKVGEKIRLYINNVGPNEVSSFHVVGTVFDDVYLDGNPNNHLQGMQTVMLPASGGAVVEFTVTRPGTYPIVTHQFNHAQKGAVAMLKVTETGED 315
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3WNJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (A4IL26_GEOTN | A4IL26)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0050421    nitrite reductase (NO-forming) activity    Catalysis of the reaction: nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+.
    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:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
    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

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UniProtKB/TrEMBL
        A4IL26_GEOTN | A4IL26: 3wkp 3wkq 3wni 3x1e 3x1f 3x1g 3x1n 4ysa 4ysd 4yso 4ysp 4ysq 4ysr 4yss 4yst 4ysu 4zk8

(-) Related Entries Specified in the PDB File

3wni