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(-) Description

Title :  STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE REDUCED WITH ASCORBATE
 
Authors :  M. E. P. Murphy, E. T. Adman, S. Turley
Date :  07 Aug 97  (Deposition) - 25 Feb 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Oxidoreductase, Nitrite, Copper, Denitrification (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Murphy, S. Turley, E. T. Adman
Structure Of Nitrite Bound To Copper-Containing Nitrite Reductase From Alcaligenes Faecalis. Mechanistic Implications.
J. Biol. Chem. V. 272 28455 1997
PubMed-ID: 9353305  |  Reference-DOI: 10.1074/JBC.272.45.28455
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NITRITE REDUCTASE
    Cellular Location: PERIPLASM
    Chains: A, B, C
    EC Number: 1.7.99.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cellular Location: PERIPLASM
    Expression System Plasmid: PNIR701
    Expression System Strain: JM-105
    Expression System Taxid: 562
    Organism Scientific: ALCALIGENES FAECALIS
    Organism Taxid: 511
    Strain: S-6

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1CU6Ligand/IonCOPPER (II) ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:95 , CYS A:136 , HIS A:145 , MET A:150BINDING SITE FOR RESIDUE CU A 501
2AC2SOFTWAREASP A:98 , HIS A:100 , HIS A:135 , HIS B:306BINDING SITE FOR RESIDUE CU A 502
3AC3SOFTWAREHIS B:95 , CYS B:136 , HIS B:145 , MET B:150BINDING SITE FOR RESIDUE CU B 501
4AC4SOFTWAREASP B:98 , HIS B:100 , HIS B:135 , HIS C:306BINDING SITE FOR RESIDUE CU B 502
5AC5SOFTWAREHIS C:95 , CYS C:136 , HIS C:145 , MET C:150BINDING SITE FOR RESIDUE CU C 501
6AC6SOFTWAREILE A:257 , HIS A:306 , ASP C:98 , HIS C:100 , HIS C:135BINDING SITE FOR RESIDUE CU C 502
7CU1UNKNOWNHIS A:95 , CYS A:136 , HIS A:145 , MET A:150COPPER SITE.
8CU3UNKNOWNHIS B:95 , CYS B:136 , HIS B:145 , MET B:150COPPER SITE.
9CU5UNKNOWNHIS C:95 , CYS C:136 , HIS C:145 , MET C:150COPPER SITE.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1AQ8)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Pro A:22 -Pro A:23
2Val A:68 -Pro A:69
3Pro B:22 -Pro B:23
4Val B:68 -Pro B:69
5Pro C:22 -Pro C:23
6Val C:68 -Pro C:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AQ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1AQ8)

(-) Exons   (0, 0)

(no "Exon" information available for 1AQ8)

(-) 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:331
 aligned with NIR_ALCFA | P38501 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:331
                                    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       344       354       364       374 
            NIR_ALCFA    45 IAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 375
               SCOP domains d1aq8a1 A:9-166 Nitrite reductase, NIR                                                                                                                        d1aq8a2 A:167-339 Nitrite reductase, NIR                                                                                                                                      SCOP domains
               CATH domains --1aq8A01 A:11-158 Cupredoxins -  blue copper proteins                                                                                                1aq8A02 A:159-325 Cupredoxins -  blue copper proteins                                                                                                                  -------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....................eeeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee.................hhhhhhh......eeeeeeee....eeeeee......hhhhhhh..eeeeeee................eeeeeeeeee...............hhhhhhhhhhhhhh....eeee............eeee...eeeeeeee......eeee.....eee.....................eeeeeeee....eeeeeee..hhhhh....eeeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1aq8 A   9 IAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 339
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338 


Chain B from PDB  Type:PROTEIN  Length:331
 aligned with NIR_ALCFA | P38501 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:331
                                    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       344       354       364       374 
            NIR_ALCFA    45 IAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 375
               SCOP domains d1aq8b1 B:9-166 Nitrite reductase, NIR                                                                                                                        d1aq8b2 B:167-339 Nitrite reductase, NIR                                                                                                                                      SCOP domains
               CATH domains --1aq8B01 B:11-158 Cupredoxins -  blue copper proteins                                                                                                1aq8B02 B:159-325 Cupredoxins -  blue copper proteins                                                                                                                  -------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....................eeeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee.................hhhhhhh......eeeeeeee....eeeeee......hhhhh....eeeeeee................eeeeeeeeee...............hhhhhhhhhhhhhh....eeee............eeee...eeeeeeee......eeee.....eee.....................eeeeeeee....eeeeeee..hhhhh....eeeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1aq8 B   9 IAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 339
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338 


Chain C from PDB  Type:PROTEIN  Length:331
 aligned with NIR_ALCFA | P38501 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:331
                                    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       344       354       364       374 
            NIR_ALCFA    45 IAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 375
               SCOP domains d1aq8c1 C:9-166 Nitrite reductase, NIR                                                                                                                        d1aq8c2 C:167-339 Nitrite reductase, NIR                                                                                                                                      SCOP domains
               CATH domains --1aq8C01 C:11-158 Cupredoxins -  blue copper proteins                                                                                                1aq8C02 C:159-325 Cupredoxins -  blue copper proteins                                                                                                                  -------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee.................hhhhhhh......eeeeeeee....eeeeee......hhhhhhh..eeeeeee................eeeeeeeeee...............hhhhhhhhhhhhhh....eeee............eeee...eeeeeeee......eeee.....eee.....................eeeeeeee....eeeeeee..hhhhh....eeeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1aq8 C   9 IAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 339
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338
   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  (1, 6)

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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AQ8)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (NIR_ALCFA | P38501)
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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  1aq8
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  NIR_ALCFA | P38501
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  1.7.99.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        NIR_ALCFA | P38501: 1as6 1as7 1as8 1et5 1et7 1et8 1j9q 1j9r 1j9s 1j9t 1l9o 1l9p 1l9q 1l9r 1l9s 1l9t 1npj 1npn 1ntd 1sjm 1snr 1zdq 1zds 2afn 2b08 2e86 2fjs 2p80 2pp7 2pp8 2pp9 2ppa 2ppc 2ppd 2ppe 2ppf 3h4f 3h4h 3h56 4ysc 4yse 5d4h 5d4i 5d4j 5f7a 5f7b

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1AQ8)