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(-) Description

Title :  STRUCTURE OF ALCALIGENES XYLOSOXIDANS IN SPACE GROUP R3 - 1 OF 2
 
Authors :  M. A. Hough, S. V. Antonyuk, R. W. Strange, R. R. Eady, S. S. Hasnain
Date :  22 Jan 08  (Deposition) - 05 Feb 08  (Release) - 29 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Denitrification, Nitrite Reductase, Ordered Mechanism, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Hough, S. V. Antonyuk, R. W. Strange, R. R. Eady, S. S. Hasnain
Crystallography With Online Optical And X-Ray Absorption Spectroscopies Demonstrates An Ordered Mechanism In Copper Nitrite Reductase.
J. Mol. Biol. V. 378 353 2008
PubMed-ID: 18353369  |  Reference-DOI: 10.1016/J.JMB.2008.01.097

(-) Compounds

Molecule 1 - DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 25-360
    Organism Scientific: ACHROMOBACTER XYLOSOXIDANS
    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
2PG41Ligand/IonTETRAETHYLENE GLYCOL
3ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2PG43Ligand/IonTETRAETHYLENE GLYCOL
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 501
2AC2SOFTWAREASP A:92 , HIS A:94 , HIS A:129 , HIS A:300 , HOH A:2067BINDING SITE FOR RESIDUE CU A 502
3AC3SOFTWAREHIS A:165 , ASP A:167 , GLU A:195 , HOH A:2229BINDING SITE FOR RESIDUE ZN A 888
4AC4SOFTWAREALA A:296 , PHE A:306 , ALA A:311 , HIS A:313BINDING SITE FOR RESIDUE PG4 A 999

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VM3)

(-) 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 2VM3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VM3)

(-) Exons   (0, 0)

(no "Exon" information available for 2VM3)

(-) 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:333
 aligned with O68601_ALCXX | O68601 from UniProtKB/TrEMBL  Length:360

    Alignment length:333
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356   
         O68601_ALCXX    27 ADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIP 359
               SCOP domains d2vm3a1 A:3-159 Nitrite reductase, NIR                                                                                                                       d2vm3a2 A:160-335 Nitrite reductase, NIR                                                                                                                                         SCOP domains
               CATH domains 2vm3A01 A:3-152 Cupredoxins -  blue copper proteins                                                                                                   2vm3A02 A:153-319 Cupredoxins -  blue copper proteins                                                                                                                  ---------------- CATH domains
               Pfam domains -----------------------------------Cu-oxidase_3-2vm3A02 A:38-155                                                                                         ------------Cu-oxidase-2vm3A01 A:168-320                                                                                                                             --------------- Pfam domains
         Sec.struct. author .....eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee................eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eee....eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vm3 A   3 ADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIP 335
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
   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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 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 2vm4 2vmj 2vn3 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
2vm4 STRUCTURE OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE IN SPACE GROUP R3 - 2 OF 2