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(-) Description

Title :  NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
 
Authors :  F. E. Dodd, J. Vanbeeumen, R. R. Eady, S. S. Hasnain
Date :  28 Oct 98  (Deposition) - 04 Nov 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Nitrite Reductase, Blue Copper, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. E. Dodd, J. Van Beeumen, R. R. Eady, S. S. Hasnain
X-Ray Structure Of A Blue-Copper Nitrite Reductase In Two Crystal Forms. The Nature Of The Copper Sites, Mode Of Substrate Binding And Recognition By Redox Partner.
J. Mol. Biol. V. 282 369 1998
PubMed-ID: 9735294  |  Reference-DOI: 10.1006/JMBI.1998.2007

(-) Compounds

Molecule 1 - PROTEIN (NITRITE REDUCTASE)
    Atcc: NCIMB 11015
    Cellular Location: PERIPLASM
    Chains: A
    Collection: NCIMB 11015
    EC Number: 1.7.99.3
    Organism Scientific: ACHROMOBACTER XYLOSOXIDANS
    Organism Taxid: 85698
    Other Details: COPPER, CHLORIDE
    Strain: XYLOSOXIDANS

 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, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CU2Ligand/IonCOPPER (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CU-1Ligand/IonCOPPER (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:89 , CYS A:130 , HIS A:139 , MET A:144BINDING SITE FOR RESIDUE CU A 501
2AC2SOFTWAREHIS A:94 , HIS A:129 , HIS A:300 , CL A:503BINDING SITE FOR RESIDUE CU A 502
3AC3SOFTWAREHIS A:129 , ILE A:251 , HIS A:300 , CU A:502BINDING SITE FOR RESIDUE CL A 503
4CUAAUTHORCU A:501 , HIS A:89 , CYS A:130 , HIS A:139 , MET A:144TYPE I COPPER SITE
5CUBAUTHORCU A:502 , HIS A:94 , HIS A:129 , CL A:503TYPE II COPPER SITE (ADDITIONAL HIS 300 FROM ADJACENT MONOMER)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:16 -Pro A:17
2Met A:62 -Pro A:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NDT)

(-) 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:336
 aligned with O68601_ALCXX | O68601 from UniProtKB/TrEMBL  Length:360

    Alignment length:336
                                    34        44        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      
         O68601_ALCXX    25 QDADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIPR 360
               SCOP domains d1ndta1 A:1-159 Nitrite reductase, NIR                                                                                                                         d1ndta2 A:160-336 Nitrite reductase, NIR                                                                                                                                          SCOP domains
               CATH domains -1ndtA01 A:2-152 Cupredoxins -  blue copper proteins                                                                                                    1ndtA02 A:153-319 Cupredoxins -  blue copper proteins                                                                                                                  ----------------- CATH domains
               Pfam domains -------------------------------------Cu-oxidase_3-1ndtA02 A:38-155                                                                                         ------------Cu-oxidase-1ndtA01 A:168-320                                                                                                                             ---------------- Pfam domains
         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................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ndt A   1 ADADSLPHTKVTLVAPPQVHPHEQATASGPKVTEFTMTIEEKKMVIDDSGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPSGMVPWHVVSGMSGTLMVLPRDGLKDPAGAPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTASVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHISVEGKWNDDLMKQIKAPAPIPA 336
                                    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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: CU_oxidase (192)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (O68601_ALCXX | O68601)
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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  1ndt
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 Related Entries

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

UniProtKB/TrEMBL
        O68601_ALCXX | O68601: 1bq5 1gs6 1gs7 1gs8 1hau 1haw 1oe1 1oe2 1oe3 1wa0 1wa1 1wa2 1wae 2bo0 2bp0 2bp8 2jfc 2vm3 2vm4 2vmj 2vn3 2vw4 2vw6 2vw7 2xwz 2xx0 2xx1 2xxf 2xxg 2zon 4csp 4csz 5b1j 5b1k

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