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(-) Description

Title :  CRYSTAL STRUCTURE OF ACHROMOBACTER CYCLOCLASTES CU NITRITE REDUCTASE WITH BOUND NO
 
Authors :  M. A. Hough, S. V. Antonyuk
Date :  07 Dec 10  (Deposition) - 16 Feb 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Oxidoreductase, Denitrification (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. V. Antonyuk, M. A. Hough
Monitoring And Validating Active Site Redox States In Protein Crystals.
Biochim. Biophys. Acta V. 1814 778 2011
PubMed-ID: 21215826  |  Reference-DOI: 10.1016/J.BBAPAP.2010.12.017

(-) Compounds

Molecule 1 - COPPER-CONTAINING NITRITE REDUCTASE
    Chains: A
    EC Number: 1.7.2.1
    Organism Scientific: ACHROMOBACTER CYCLOCLASTES
    Organism Taxid: 223
    Synonym: CU-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  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CU2Ligand/IonCOPPER (II) ION
3NO1Ligand/IonNITRIC OXIDE
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 18)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2CU-1Ligand/IonCOPPER (II) ION
3NO-1Ligand/IonNITRIC OXIDE
4SO412Ligand/IonSULFATE 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 500
2AC2SOFTWAREHIS A:100 , HIS A:135 , HIS A:306 , NO A:502BINDING SITE FOR RESIDUE CU A 501
3AC3SOFTWAREASP A:98 , HIS A:100 , HIS A:135 , HIS A:255 , ILE A:257 , HIS A:306 , CU A:501BINDING SITE FOR RESIDUE NO A 502
4AC4SOFTWARETRP A:265 , THR A:267 , GLY A:268 , LYS A:269 , ASN A:272 , ASP A:275 , GLN A:278 , HOH A:2187 , HOH A:2230BINDING SITE FOR RESIDUE ACT A 503
5AC5SOFTWAREHIS A:60 , GLU A:197 , THR A:198 , PRO A:199BINDING SITE FOR RESIDUE ACT A 504
6AC6SOFTWARELYS A:33 , ASP A:188 , GLU A:189BINDING SITE FOR RESIDUE SO4 A 505
7AC7SOFTWARELYS A:125 , THR A:127 , ARG A:296 , HOH A:2224BINDING SITE FOR RESIDUE SO4 A 506
8AC8SOFTWARELYS A:128 , ARG A:271 , HOH A:2231 , HOH A:2232BINDING SITE FOR RESIDUE SO4 A 507
9AC9SOFTWARETHR A:228 , GLY A:229 , ASP A:230 , HIS A:231 , HOH A:2234BINDING SITE FOR RESIDUE SO4 A 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y1A)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:22 -Pro A:23
2Val A:68 -Pro A:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y1A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y1A)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y1A)

(-) 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:332
 aligned with NIR_ACHCY | P25006 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:332
                                    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 DISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPAS 377
               SCOP domains d2y1aa1 A:8-166 Nitrite reductase, NIR                                                                                                                         d2y1aa2 A:167-339 Nitrite reductase, NIR                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------Cu-oxidase_3-2y1aA02 A:44-161                                                                                         ------------Cu-oxidase-2y1aA01 A:174-326                                                                                                                             ------------- Pfam domains
         Sec.struct. author hhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee.......eeeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y1a A   8 DISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPAS 339
                                    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)
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  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  (0, 0)

(no "CATH Domain" information available for 2Y1A)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: CU_oxidase (192)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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  1.7.2.1
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1kcb CRYSTAL STRUCTURE OF A NO-FORMING NITRITE REDUCTASE MUTANT:AN ANALOG OF A TRANSITION STATE IN ENZYMATIC REACTION
1nia
1nib
1nic
1nid
1nie
1nif
1rzp CRYSTAL STRUCTURE OF C-TERMINAL DESPENTAPEPTIDE NITRITEREDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT PH6.2
1rzq CRYSTAL STRUCTURE OF C-TERMINAL DESPENTAPEPTIDE NITRITEREDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT PH5.0
2avf CRYSTAL STRUCTURE OF C-TERMINAL DESUNDECAPEPTIDE NITRITEREDUCTASE FROM ACHROMOBACTER CYCLOCLASTES
2bw4 ATOMIC RESOLUTION STRUCTURE OF RESTING STATE OF THE ALCALIGENES CYCLOCLASTES CU NITRITE REDUCTASE
2bw5 ATOMIC RESOLUTION STRUCTURE OF NO-BOUND ALCALIGENES CYCLOCLASTES CU NITRITE REDUCTASE
2bwd ATOMIC RESOLUTION STRUCTURE OF ACHROMOBACTER CYCLOCLASTES CU NITRITE REDUCTASE WITH ENDOGENOUSLY BOUND NITRATE AND NO
2bwi ATOMIC RESOLUTION STRUCTURE OF NITRITE -SOAKED ACHROMOBACTER CYCLOCLASTES CU NITRITE REDUCTASE
2nrd