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(-) Description

Title :  CRYSTALLOGRAPHIC STRUCTURE OF A SUBSTRATE BOUND BLUE COPPER NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
 
Authors :  F. E. Dodd, S. S. Hasnain, Z. H. L. Abraham, R. R. Eady, B. E. Smith
Date :  23 Jan 97  (Deposition) - 07 Jul 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Blue Copper Nitrite Reductase, Copper Protein, Nitrite Reduction, Reductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. E. Dodd, S. S. Hasnain, Z. H. Abraham, R. R. Eady, B. E. Smith
Structures Of A Blue-Copper Nitrite Reductase And Its Substrate-Bound Complex.
Acta Crystallogr. , Sect. D V. 53 406 1997
PubMed-ID: 15299906  |  Reference-DOI: 10.1107/S0907444997002667
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NITRITE REDUCTASE
    Chains: A, B, C
    EC Number: 1.7.99.3
    Organism Scientific: ACHROMOBACTER XYLOSOXIDANS
    Organism Taxid: 85698
    Other Details: BACTERIAL
    Strain: NCIMB 11015
    Synonym: NIR

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1CU6Ligand/IonCOPPER (II) ION
2NO23Ligand/IonNITRITE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2NO21Ligand/IonNITRITE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2NO21Ligand/IonNITRITE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2NO21Ligand/IonNITRITE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1UNKNOWNHIS A:95 , CYS A:136 , HIS A:145 , MET A:150MONOMER A TYPE 1 COPPER SITE.
02AC2UNKNOWNHIS A:100 , HIS A:135 , HIS A:306 , NO2 A:503MONOMER A TYPE 2 COPPER SITE.
03AC3SOFTWAREHIS A:95 , CYS A:136 , HIS A:145 , MET A:150BINDING SITE FOR RESIDUE CU A 501
04AC4SOFTWAREHIS A:100 , HIS A:135 , NO2 A:503 , HIS B:306BINDING SITE FOR RESIDUE CU A 502
05AC5SOFTWAREHIS A:100 , HIS A:135 , CU A:502 , HIS B:306BINDING SITE FOR RESIDUE NO2 A 503
06AC6SOFTWAREHIS B:95 , CYS B:136 , HIS B:145 , MET B:150BINDING SITE FOR RESIDUE CU B 501
07AC7SOFTWAREHIS B:100 , HIS B:135 , NO2 B:503 , HIS C:306BINDING SITE FOR RESIDUE CU B 502
08AC8SOFTWAREHIS B:100 , HIS B:135 , CU B:502 , HIS C:306BINDING SITE FOR RESIDUE NO2 B 503
09AC9SOFTWAREHIS C:95 , CYS C:136 , HIS C:145 , MET C:150BINDING SITE FOR RESIDUE CU C 501
10AD1SOFTWAREHIS A:306 , HIS C:100 , HIS C:135 , NO2 C:503BINDING SITE FOR RESIDUE CU C 502
11AD2SOFTWAREHIS A:306 , HIS C:100 , HIS C:135 , CU C:502BINDING SITE FOR RESIDUE NO2 C 503
12BC1UNKNOWNHIS B:95 , CYS B:136 , HIS B:145 , MET B:150MONOMER B TYPE 1 COPPER SITE.
13BC2UNKNOWNHIS B:100 , HIS B:135 , HIS B:306 , NO2 B:503MONOMER B TYPE 2 COPPER SITE.
14CC1UNKNOWNHIS C:95 , CYS C:136 , HIS C:145 , MET C:150MONOMER C TYPE 1 COPPER SITE.
15CC2UNKNOWNHIS C:100 , HIS C:135 , HIS C:306 , NO2 C:503MONOMER C TYPE 2 COPPER SITE.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NDS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NDS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NDS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NDS)

(-) Exons   (0, 0)

(no "Exon" information available for 1NDS)

(-) 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:330
 aligned with NIR_ALCXX | P81445 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:330
                                    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
            NIR_ALCXX     1 GLPRVAVDLVAPPLVHPHSQVAAGAPKVVQFRMSIEEKKMVADDDGTTAQAMTFNGSVPGPTLVVHEGDYIELTLVNPATNSMPHNVDFHAATGALGGAGLTQVVPGQEAVLRFKADRSGTFVYHCAPAGMVPWHVVSGMNGALMVLPRDGLRDAAGAALAYDRVYTIGESDLYVPKAADGNYSDYPALASAYADTVAVMRTLTPSHAVFNGAVGALTGANALTAAVGESVLIIHSQANRDSRPHLIGGHGDWVWTTGKFANPPQLNMETWFIPGGSAAAALYTFKQPGTYAYLSHNLIEAMELGAAAQASVEGQWDDDLMTSVAAPGPA 330
               SCOP domains d1ndsa1 A:11-166 Nitrite reductase, NIR                                                                                                                     d1ndsa2 A:167-340 Nitrite reductase, NIR                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................................................................................................................................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nds A  11 GLPRVAVDLVAPPLVHPHSQVAAGAPKVVQFRMSIEEKKMVADDDGTTAQAMTFNGSVPGPTLVVHEGDYIELTLVNPATNSMPHNVDFHAATGALGGAGLTQVVPGQEAVLRFKADRSGTFVYHCAPAGMVPWHVVSGMNGALMVLPRDGLRDAAGAALAYDRVYTIGESDLYVPKAADGNYSDYPALASAYADTVAVMRTLTPSHAVFNGAVGALTGANALTAAVGESVLIIHSQANRDSRPHLIGGHGDWVWTTGKFANPPQLNMETWFIPGGSAAAALYTFKQPGTYAYLSHNLIEAMELGAAAQASVEGQWDDDLMTSVAAPGPA 340
                                    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


Chain B from PDB  Type:PROTEIN  Length:330
 aligned with NIR_ALCXX | P81445 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:330
                                    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
            NIR_ALCXX     1 GLPRVAVDLVAPPLVHPHSQVAAGAPKVVQFRMSIEEKKMVADDDGTTAQAMTFNGSVPGPTLVVHEGDYIELTLVNPATNSMPHNVDFHAATGALGGAGLTQVVPGQEAVLRFKADRSGTFVYHCAPAGMVPWHVVSGMNGALMVLPRDGLRDAAGAALAYDRVYTIGESDLYVPKAADGNYSDYPALASAYADTVAVMRTLTPSHAVFNGAVGALTGANALTAAVGESVLIIHSQANRDSRPHLIGGHGDWVWTTGKFANPPQLNMETWFIPGGSAAAALYTFKQPGTYAYLSHNLIEAMELGAAAQASVEGQWDDDLMTSVAAPGPA 330
               SCOP domains d1ndsb1 B:11-166 Nitrite reductase, NIR                                                                                                                     d1ndsb2 B:167-340 Nitrite reductase, NIR                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................................................................................................................................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nds B  11 GLPRVAVDLVAPPLVHPHSQVAAGAPKVVQFRMSIEEKKMVADDDGTTAQAMTFNGSVPGPTLVVHEGDYIELTLVNPATNSMPHNVDFHAATGALGGAGLTQVVPGQEAVLRFKADRSGTFVYHCAPAGMVPWHVVSGMNGALMVLPRDGLRDAAGAALAYDRVYTIGESDLYVPKAADGNYSDYPALASAYADTVAVMRTLTPSHAVFNGAVGALTGANALTAAVGESVLIIHSQANRDSRPHLIGGHGDWVWTTGKFANPPQLNMETWFIPGGSAAAALYTFKQPGTYAYLSHNLIEAMELGAAAQASVEGQWDDDLMTSVAAPGPA 340
                                    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


Chain C from PDB  Type:PROTEIN  Length:330
 aligned with NIR_ALCXX | P81445 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:330
                                    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
            NIR_ALCXX     1 GLPRVAVDLVAPPLVHPHSQVAAGAPKVVQFRMSIEEKKMVADDDGTTAQAMTFNGSVPGPTLVVHEGDYIELTLVNPATNSMPHNVDFHAATGALGGAGLTQVVPGQEAVLRFKADRSGTFVYHCAPAGMVPWHVVSGMNGALMVLPRDGLRDAAGAALAYDRVYTIGESDLYVPKAADGNYSDYPALASAYADTVAVMRTLTPSHAVFNGAVGALTGANALTAAVGESVLIIHSQANRDSRPHLIGGHGDWVWTTGKFANPPQLNMETWFIPGGSAAAALYTFKQPGTYAYLSHNLIEAMELGAAAQASVEGQWDDDLMTSVAAPGPA 330
               SCOP domains d1ndsc1 C:11-166 Nitrite reductase, NIR                                                                                                                     d1ndsc2 C:167-340 Nitrite reductase, NIR                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................................................................................................................................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nds C  11 GLPRVAVDLVAPPLVHPHSQVAAGAPKVVQFRMSIEEKKMVADDDGTTAQAMTFNGSVPGPTLVVHEGDYIELTLVNPATNSMPHNVDFHAATGALGGAGLTQVVPGQEAVLRFKADRSGTFVYHCAPAGMVPWHVVSGMNGALMVLPRDGLRDAAGAALAYDRVYTIGESDLYVPKAADGNYSDYPALASAYADTVAVMRTLTPSHAVFNGAVGALTGANALTAAVGESVLIIHSQANRDSRPHLIGGHGDWVWTTGKFANPPQLNMETWFIPGGSAAAALYTFKQPGTYAYLSHNLIEAMELGAAAQASVEGQWDDDLMTSVAAPGPA 340
                                    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
   Legend:   → Mismatch (orange background)
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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, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1NDS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1NDS)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (NIR_ALCXX | P81445)
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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        NIR_ALCXX | P81445: 1ndr

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