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(-) Description

Title :  NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
 
Authors :  K. Sato, S. J. Firbank, C. Li, M. J. Banfield, C. Dennison
Date :  30 Jan 08  (Deposition) - 23 Dec 08  (Release) - 23 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Cupredoxin, Type 1 Copper, Type 2 Copper, Oxidoreductase, Electron Transfer, Copper-Containing Nitrite Reductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Sato, S. J. Firbank, C. Li, M. J. Banfield, C. Dennison
The Importance Of The Long Type 1 Copper-Binding Loop Of Nitrite Reductase For Structure And Function.
Chemistry V. 14 5820 2008
PubMed-ID: 18491346  |  Reference-DOI: 10.1002/CHEM.200701997

(-) Compounds

Molecule 1 - DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: RESIDUES 25-360
    Organism Scientific: ALCALIGENES XYLOSOXYDANS XYLOSOXYDANS
    Organism Taxid: 85698
    Synonym: NITRITE REDUCTASE, 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  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CU2Ligand/IonCOPPER (II) ION
2SO41Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2SO43Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:89 , CYS A:130 , HIS A:139 , MET A:144BINDING SITE FOR RESIDUE CU A 401
2AC2SOFTWAREHIS A:94 , HIS A:129 , HIS A:300 , HOH A:2052BINDING SITE FOR RESIDUE CU A 402
3AC3SOFTWAREHIS A:165 , ASP A:167 , GLU A:195 , HOH A:2161BINDING SITE FOR RESIDUE ZN A 403
4AC4SOFTWAREALA A:3 , ASP A:4 , LEU A:6 , HIS A:8BINDING SITE FOR RESIDUE SO4 A 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VN3)

(-) 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 2VN3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VN3)

(-) Exons   (0, 0)

(no "Exon" information available for 2VN3)

(-) 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 d2vn3a1 A:1-159 automated matches                                                                                                                              d2vn3a2 A:160-336 automated matches                                                                                                                                               SCOP domains
               CATH domains -2vn3A01 A:2-152 Cupredoxins -  blue copper proteins                                                                                                    2vn3A02 A:153-319 Cupredoxins -  blue copper proteins                                                                                                                  ----------------- CATH domains
               Pfam domains -------------------------------------Cu-oxidase_3-2vn3A02 A:38-155                                                                                         ------------Cu-oxidase-2vn3A01 A:168-320                                                                                                                             ---------------- Pfam domains
         Sec.struct. author .hhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee................eeeeeeeeee...............hhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vn3 A   1 QDADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIPR 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)
    → 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, 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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  O68601_ALCXX | O68601
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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 1ndt 1oe1 1oe2 1oe3 1wa0 1wa1 1wa2 1wae 2bo0 2bp0 2bp8 2jfc 2vm3 2vm4 2vmj 2vw4 2vw6 2vw7 2xwz 2xx0 2xx1 2xxf 2xxg 2zon 4csp 4csz 5b1j 5b1k

(-) Related Entries Specified in the PDB File

1bq5 NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS GIFU 1051
1gs6 CRYSTAL STRUCTURE OF M144A MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1gs7 CRYSTAL STRUCTURE OF H254F MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1gs8 CRYSTAL STRUCTURE OF M144A MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1hau X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND IN COPPER FREE FORM AT 1.9E RESOLUTION
1haw X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND IN COPPER FREE FORM AT 1.9E RESOLUTION
1ndt NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
1oe1 ATOMIC RESOLUTION STRUCTURE OF THE WILDTYPE NATIVE NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
1oe2 ATOMIC RESOLUTION STRUCTURE OF D92E MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1oe3 ATOMIC RESOLUTION STRUCTURE OF 'HALF APO' NIR
1wa0 CRYSTAL STRUCTURE OF W138H MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1wa1 CRYSTAL STRUCTURE OF H313Q MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1wa2 CRYSTAL STRUCTURE OF H313Q MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE WITH NITRITE BOUND
1wae CRYSTAL STRUCTURE OF H129V MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
2bo0 CRYSTAL STRUCTURE OF THE C130A MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
2bp0 M144L MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
2bp8 M144Q STRUCTURE OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
2jfc M144L MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS IN SPACE GROUP P212121
2vm3 STRUCTURE OF ALCALIGENES XYLOSOXIDANS IN SPACE GROUP R3 - 1 OF 2
2vm4 STRUCTURE OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE IN SPACE GROUP R3 - 2 OF 2
2vmj TYPE 1 COPPER-BINDING LOOP OF NITRITE REDUCTASE MUTANT: 130-CAPEGMVPWHVVSGM-144 TO 130-CTPHPFM-136