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(-) Description

Title :  COPPER-CONTAINING NITRITE REDUCTASE FROM GEOBACILLUS THERMODENITRIFICANS IN COMPLEX WITH FORMATE
 
Authors :  Y. Fukuda, T. Inoue
Date :  29 Oct 13  (Deposition) - 11 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.15
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Greek Key Beta Barrel, Nitrite Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Fukuda, T. Inoue
Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans In Complex With Formate
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
    Synonym: COPPER-CONTAINING NITRITE REDUCTASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 21)

Asymmetric Unit (6, 21)
No.NameCountTypeFull Name
1CU6Ligand/IonCOPPER (II) ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3FMT9Ligand/IonFORMIC ACID
4MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NA1Ligand/IonSODIUM ION
6SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 42)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3FMT27Ligand/IonFORMIC ACID
4MPD9Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NA-1Ligand/IonSODIUM ION
6SO43Ligand/IonSULFATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
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 , FMT A:408 , HOH A:872BINDING SITE FOR RESIDUE CU A 402
03AC3SOFTWAREHIS A:42 , GLU A:53 , HIS A:83 , FMT A:410 , HOH A:736 , HOH A:844BINDING SITE FOR RESIDUE CU A 403
04AC4SOFTWAREHIS A:39 , FMT A:414BINDING SITE FOR RESIDUE CU A 404
05AC5SOFTWAREPRO A:191 , GLU A:239 , HIS A:298 , FMT A:413 , HOH A:716 , HOH A:784 , HOH A:847BINDING SITE FOR RESIDUE CU A 405
06AC6SOFTWAREASP A:167 , FMT A:411 , HOH A:718 , HOH A:797 , HOH A:823BINDING SITE FOR RESIDUE CU A 406
07AC7SOFTWAREGLU A:78 , HOH A:683BINDING SITE FOR RESIDUE NA A 407
08AC8SOFTWAREHIS A:134 , HIS A:244 , VAL A:246 , HIS A:294 , PHE A:296 , CU A:402 , FMT A:409 , HOH A:525 , HOH A:872 , HOH A:873BINDING SITE FOR RESIDUE FMT A 408
09AC9SOFTWARELYS A:138 , FMT A:408 , HOH A:595 , HOH A:724 , HOH A:873BINDING SITE FOR RESIDUE FMT A 409
10BC1SOFTWAREHIS A:42 , GLU A:53 , GLY A:57 , HIS A:83 , CU A:403 , HOH A:546 , HOH A:700 , HOH A:736 , HOH A:803 , HOH A:844BINDING SITE FOR RESIDUE FMT A 410
11BC2SOFTWAREASP A:167 , CU A:406 , HOH A:730 , HOH A:797 , HOH A:823BINDING SITE FOR RESIDUE FMT A 411
12BC3SOFTWAREASN A:16 , VAL A:17 , ILE A:18 , HIS A:21 , TRP A:63 , TYR A:180BINDING SITE FOR RESIDUE FMT A 412
13BC4SOFTWAREGLN A:187 , VAL A:190 , PRO A:191 , ASN A:297 , HIS A:298 , LYS A:301 , CU A:405 , HOH A:665 , HOH A:716 , HOH A:784 , HOH A:847BINDING SITE FOR RESIDUE FMT A 413
14BC5SOFTWAREPRO A:38 , HIS A:39 , LYS A:218 , CU A:404 , HOH A:802 , HOH A:853BINDING SITE FOR RESIDUE FMT A 414
15BC6SOFTWARELYS A:32 , MET A:33 , GLU A:34 , HIS A:42 , GLU A:44 , HOH A:866 , HOH A:867BINDING SITE FOR RESIDUE FMT A 415
16BC7SOFTWAREASN A:258 , ASN A:260 , GLN A:264 , HOH A:547 , HOH A:683 , HOH A:835BINDING SITE FOR RESIDUE FMT A 416
17BC8SOFTWAREASP A:163 , VAL A:166 , ASP A:167 , ARG A:168 , GLU A:169 , ARG A:229 , HOH A:672 , HOH A:743BINDING SITE FOR RESIDUE MPD A 417
18BC9SOFTWAREASP A:55 , SER A:192 , TYR A:193 , THR A:212 , GLN A:300 , LYS A:301 , GLY A:302 , HOH A:655BINDING SITE FOR RESIDUE MPD A 418
19CC1SOFTWAREALA A:200 , LYS A:202 , HOH A:701BINDING SITE FOR RESIDUE MPD A 419
20CC2SOFTWAREARG A:285 , HOH A:585 , HOH A:592 , HOH A:664 , HOH A:837BINDING SITE FOR RESIDUE EDO A 420
21CC3SOFTWAREHIS A:262 , LEU A:263 , HOH A:854 , HOH A:855BINDING SITE FOR RESIDUE SO4 A 421

(-) SS Bonds  (0, 0)

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

(-) 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 3WKQ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WKQ)

(-) 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:299
 aligned with A4IL26_GEOTN | A4IL26 from UniProtKB/TrEMBL  Length:352

    Alignment length:299
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334         
         A4IL26_GEOTN    45 NVIAAHKGVNQAPVPLKMERVGPHDVHIEMTAQITDIEIDKGKIYKAWTFNGQAPGPLVVVNEGDTIHFTLKNMDPVVPHSMDFHAVHASPSKDFIDVMPNKSGTFTYPANKPGVFMYHCGTKPVLQHIANGMHGVIIVKPKNGYPTDKEVDREYVLIQNEWYKYNDMNDFQNGVPSYVVFSSKALKPGDPNTNGDTFTLKEKPLLAKVGEKIRLYINNVGPNEVSSFHVVGTVFDDVYLDGNPNNHLQGMQTVMLPASGGAVVEFTVTRPGTYPIVTHQFNHAQKGAVAMLKVTETGE 343
               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...eeeeeee.............hhhhhh.eeee...eeeeeeeeee....eeeee....eeeeee......eeeee..eee....eeeeeee....eeeeeee.hhhhhhh..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wkq A  16 NVIAAHKGVNQAPVPLKMERVGPHDVHIEMTAQITDIEIDKGKIYKAWTFNGQAPGPLVVVNEGDTIHFTLKNMDPVVPHSMDFHAVHASPSKDFIDVMPNKSGTFTYPANKPGVFMYHCGTKPVLQHIANGMHGVIIVKPKNGYPTDKEVDREYVLIQNEWYKYNDMNDFQNGVPSYVVFSSKALKPGDPNTNGDTFTLKEKPLLAKVGEKIRLYINNVGPNEVSSFHVVGTVFDDVYLDGNPNNHLQGMQTVMLPASGGAVVEFTVTRPGTYPIVTHQFNHAQKGAVAMLKVTETGE 314
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305
   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 3WKQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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

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

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

(-) Related Entries Specified in the PDB File

3wko 3wkp