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(-) Description

Title :  CU-CONTAINING NITRITE REDUCTASE
 
Authors :  F. Jacobson, H. Guo, K. Olesen, M. Okvist, R. Neutze, L. Sjolin
Date :  27 Jun 05  (Deposition) - 02 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Copper Protein, Nitrite Reduction, Denitrification, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Jacobson, H. Guo, K. Olesen, M. Okvist, R. Neutze, L. Sjolin
Structures Of The Oxidized And Reduced Forms Of Nitrite Reductase From Rhodobacter Sphaeroides 2. 4. 3 At High Ph: Changes In The Interactions Of The Type 2 Copper.
Acta Crystallogr. , Sect. D V. 61 1190 2005
PubMed-ID: 16131751  |  Reference-DOI: 10.1107/S0907444905017488

(-) Compounds

Molecule 1 - COPPER-CONTAINING NITRITE REDUCTASE
    Chains: A
    EC Number: 1.7.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET17B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 44-371
    Gene: NIRK
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Synonym: CU-NIR

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CU2Ligand/IonCOPPER (II) ION
2MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:126 , CYS A:167 , HIS A:177 , MET A:182BINDING SITE FOR RESIDUE CU A 401
2AC2SOFTWAREASP A:129 , HIS A:131 , HIS A:166 , HIS A:338BINDING SITE FOR RESIDUE CU A 402
3AC3SOFTWAREASP A:220 , THR A:224 , HOH A:557 , HOH A:558 , HOH A:559 , HOH A:568BINDING SITE FOR RESIDUE MG A 501
4AC4SOFTWAREHOH A:585 , HOH A:589 , HOH A:725 , HOH A:726 , HOH A:728BINDING SITE FOR RESIDUE MG A 502
5AC5SOFTWAREHOH A:562 , HOH A:705 , HOH A:727 , HOH A:732BINDING SITE FOR RESIDUE MG A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A3T)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:54 -Pro A:55
2Ile A:99 -Pro A:100

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A3T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A3T)

(-) Exons   (0, 0)

(no "Exon" information available for 2A3T)

(-) 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:328
 aligned with NIR_RHOS5 | Q53239 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:328
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363        
            NIR_RHOS5    44 LPRVKHTLVPPPFAHAHEQVAASGPVINEFEMRIIEKEVQLDEDAYLQAMTFDGSIPGPLMIVHEGDYVELTLINPPENTMPHNIDFHAATGALGGGGLTLINPGEKVVLRFKATRAGAFVYHCAPGGPMIPWHVVSGMAGCIMVLPRDGLKDHEGKPVRYDTVYYIGESDHYIPKDEDGTYMRFSDPSEGYEDMVAVMDTLIPSHIVFNGAVGALTGEGALKAKVGDNVLFVHSQPNRDSRPHLIGGHGDLVWETGKFHNAPERDLETWFIRGGSAGAALYKFLQPGVYAYVNHNLIEAVHKGATAHVLVEGEWDNDLMEQVVAPVG 371
               SCOP domains d2a3ta1 A:44-193 Nitrite reductase, NIR                                                                                                               d2a3ta2 A:194-371 Nitrite reductase, NIR                                                                                                                                           SCOP domains
               CATH domains 2a3tA01 A:44-190 Cupredoxins -  blue copper proteins                                                                                               2a3tA02 A:191-371 Cupredoxins -  blue copper proteins                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....................eeeeeeeeeeeeeeee..eeeeeeee.......eeeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhhh..eeeeeee................eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a3t A  44 LPRVKHTLVPPPFAHAHEQVAASGPVINEFEMRIIEKEVQLDEDAYLQAMTFDGSIPGPLMIVHEGDYVELTLINPPENTMPHNIDFHAATGALGGGGLTLINPGEKVVLRFKATRAGAFVYHCAPGGPMIPWHVVSGMAGCIMVLPRDGLKDHEGKPVRYDTVYYIGESDHYIPKDEDGTYMRFSDPSEGYEDMVAVMDTLIPSHIVFNGAVGALTGEGALKAKVGDNVLFVHSQPNRDSRPHLIGGHGDLVWETGKFHNAPERDLETWFIRGGSAGAALYKFLQPGVYAYVNHNLIEAVHKGATAHVLVEGEWDNDLMEQVVAPVG 371
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363
   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  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A3T)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (NIR_RHOS5 | Q53239)
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:0019333    denitrification pathway    The reduction of nitrate to dinitrogen by four reactions; each intermediate is transformed to the next lower oxidation state; also part of cellular bioenergetics; the nitrogen compounds can serve as terminal acceptors for electron transport phosphorylation in place of oxygen.
    GO:0042128    nitrate assimilation    The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  1.7.2.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        NIR_RHOS5 | Q53239: 1mzy 1mzz 1n70 1zv2 2dws 2dwt 2dy2

(-) Related Entries Specified in the PDB File

1zv2 OXIDISED NITRITE REDUCTASE