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(-) Description

Title :  THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES, WITH NITRITE BOUND AND WITH TYPE II CU DEPLETED
 
Authors :  E. T. Adman, J. W. Godden, S. Turley
Date :  03 Jul 95  (Deposition) - 07 Dec 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Oxidoreductase (Nitric Oxide(A)) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. T. Adman, J. W. Godden, S. Turley
The Structure Of Copper-Nitrite Reductase From Achromobacter Cycloclastes At Five Ph Values, With No2- Bound And With Type Ii Copper Depleted.
J. Biol. Chem. V. 270 27458 1995
PubMed-ID: 7499203  |  Reference-DOI: 10.1074/JBC.270.46.27458
(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 CYCLOCLASTES
    Organism Taxid: 223
    Other Details: PH 6.8 ("68")

 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  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1AUTHORHIS A:95 , CYS A:136 , HIS A:145 , MET A:150TYPE I CU (A 501) BINDING SITE IN CHAIN A
02AC2AUTHORHIS A:100 , HIS A:135 , HOH A:503TYPE II CU (A 502) BINDING SITE IN CHAIN A
03AC3SOFTWAREHIS A:95 , CYS A:136 , HIS A:145 , MET A:150BINDING SITE FOR RESIDUE CU A 501
04AC4SOFTWAREHIS A:100 , HIS A:135 , HOH A:503 , HIS B:306BINDING SITE FOR RESIDUE CU A 502
05AC5SOFTWAREHIS B:95 , CYS B:136 , HIS B:145 , MET B:150BINDING SITE FOR RESIDUE CU B 501
06AC6SOFTWAREASP B:98 , HIS B:100 , HIS B:135 , HOH B:503 , HIS C:306BINDING SITE FOR RESIDUE CU B 502
07AC7SOFTWAREHIS C:95 , CYS C:136 , HIS C:145 , MET C:150BINDING SITE FOR RESIDUE CU C 501
08AC8SOFTWAREHIS A:255 , HIS A:306 , HOH A:504 , HIS C:100 , HIS C:135BINDING SITE FOR RESIDUE CU C 502
09BC1AUTHORHIS B:95 , CYS B:136 , HIS B:145 , MET B:150TYPE I CU (B 501) BINDING SITE IN CHAIN B
10BC2AUTHORHIS B:100 , HIS B:135 , HOH B:503TYPE II CU (B 502) BINDING SITE IN CHAIN B
11CC1AUTHORHIS C:95 , CYS C:136 , HIS C:145 , MET C:150TYPE I CU (C 501) BINDING SITE IN CHAIN C
12CC2AUTHORHIS C:100 , HIS C:135 , HOH A:504TYPE II CU (C 502) BINDING SITE IN CHAIN C

(-) SS Bonds  (0, 0)

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

(-) 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 1NIB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NIB)

(-) 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:333
 aligned with NIR_ACHCY | P25006 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:333
                                    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       315       325       335       345       355       365       375   
            NIR_ACHCY    46 DISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM 378
               SCOP domains d1niba1 A:8-166 Nitrite reductase, NIR                                                                                                                         d1niba2 A:167-340 Nitrite reductase, NIR                                                                                                                                       SCOP domains
               CATH domains 1nibA01 A:8-158 Cupredoxins -  blue copper proteins                                                                                                    1nibA02 A:159-325 Cupredoxins -  blue copper proteins                                                                                                                  --------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh..eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee.................hhhh.........eeeeeeee....eeeeee......hhhhhhh..eeeeeee................eeeeeeeeee...............hhhhhhhhhhhhhh....eeee........hhh.eeee...eeeeeeee....eeeeee.....eee..............eeee...eeeeeeee....eeeeeee..hhhhh....eeeeeee.......eee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nib A   8 DISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM 340
                                    17        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       317       327       337   


Chain B from PDB  Type:PROTEIN  Length:333
 aligned with NIR_ACHCY | P25006 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:333
                                    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       315       325       335       345       355       365       375   
            NIR_ACHCY    46 DISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM 378
               SCOP domains d1nibb1 B:8-166 Nitrite reductase, NIR                                                                                                                         d1nibb2 B:167-340 Nitrite reductase, NIR                                                                                                                                       SCOP domains
               CATH domains 1nibB01 B:8-158 Cupredoxins -  blue copper proteins                                                                                                    1nibB02 B:159-325 Cupredoxins -  blue copper proteins                                                                                                                  --------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh..eee.....................eeeeeeeeeeeeee......eeeeeee.......eeeee...eeeeeeee.................hhhh.........eeeeeeee....eeeeee......hhhhh....eeeeeee................eeeeeeeeee...............hhhhhhhhhhhhhh....eeee........hhh.eeee...eeeeeeee......eeee.....eee.....................eeeeeeee....eeeeeee..hhhhh....eeeeeee.......eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nib B   8 DISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM 340
                                    17        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       317       327       337   


Chain C from PDB  Type:PROTEIN  Length:333
 aligned with NIR_ACHCY | P25006 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:333
                                    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       315       325       335       345       355       365       375   
            NIR_ACHCY    46 DISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM 378
               SCOP domains d1nibc1 C:8-166 Nitrite reductase, NIR                                                                                                                         d1nibc2 C:167-340 Nitrite reductase, NIR                                                                                                                                       SCOP domains
               CATH domains 1nibC01 C:8-158 Cupredoxins -  blue copper proteins                                                                                                    1nibC02 C:159-325 Cupredoxins -  blue copper proteins                                                                                                                  --------------- CATH domains
           Pfam domains (1) ------------------------------------Cu-oxidase_3-1nibC04 C:44-161                                                                                         ------------Cu-oxidase-1nibC01 C:174-326                                                                                                                             -------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------Cu-oxidase_3-1nibC05 C:44-161                                                                                         ------------Cu-oxidase-1nibC02 C:174-326                                                                                                                             -------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------Cu-oxidase_3-1nibC06 C:44-161                                                                                         ------------Cu-oxidase-1nibC03 C:174-326                                                                                                                             -------------- Pfam domains (3)
         Sec.struct. author .hhh..eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee.................hhhhhhh......eeeeeeee....eeeeee......hhhhhh...eeeeeee................eeeeeeeeee...............hhhhhhhhhhhhhh....eeee........hhh.eeee...eeeeeeee......eeee.....eee.....................eeeeeeee....eeeeeee..hhhhh....eeeeeee.......eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nib C   8 DISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM 340
                                    17        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       317       327       337
   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  (2, 6)

Asymmetric/Biological Unit
(-)
Clan: CU_oxidase (192)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (NIR_ACHCY | P25006)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        NIR_ACHCY | P25006: 1kcb 1nia 1nic 1nid 1nie 1nif 1rzp 1rzq 2avf 2bw4 2bw5 2bwd 2bwi 2nrd 2y1a 5akr 5i6k 5i6l 5i6m 5i6n 5i6o 5i6p

(-) Related Entries Specified in the PDB File

1nia PH 6.2
1nic PH 6.0
1nid PH 5.4 NITRITE SOAKED
1nie PH 5.0
1nif PH 5.4 TYPE II COPPER DEPLETED
2nrd PH 5.4