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(-) Description

Title :  ATOMIC RESOLUTION STRUCTURE OF NITRITE -SOAKED ACHROMOBACTER CYCLOCLASTES CU NITRITE REDUCTASE
 
Authors :  S. V. Antonyuk, R. W. Strange, G. Sawers, R. R. Eady, S. S. Hasnain
Date :  14 Jul 05  (Deposition) - 17 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Oxidoreductase, Denitrification, Catalysis, Enzyme Mechanism, Nitrate Assimilation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. V. Antonyuk, R. W. Strange, G. Sawers, R. R. Eady, S. S. Hasnain
Atomic Resolution Structures Of Resting-State, Substrate- And Product-Complexed Cu-Nitrite Reductase Provide Insight Into Catalytic Mechanism
Proc. Natl. Acad. Sci. Usa V. 102 12041 2005
PubMed-ID: 16093314  |  Reference-DOI: 10.1073/PNAS.0504207102

(-) Compounds

Molecule 1 - COPPER-CONTAINING NITRITE REDUCTASE
    Chains: A
    EC Number: 1.7.2.1
    Organism Scientific: ACHROMOBACTER CYCLOCLASTES
    Organism Taxid: 223
    Synonym: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE, 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
1ACT5Ligand/IonACETATE ION
2CU2Ligand/IonCOPPER (II) ION
3MLI1Ligand/IonMALONATE ION
4NO21Ligand/IonNITRITE ION
Biological Unit 1 (3, 21)
No.NameCountTypeFull Name
1ACT15Ligand/IonACETATE ION
2CU-1Ligand/IonCOPPER (II) ION
3MLI3Ligand/IonMALONATE ION
4NO23Ligand/IonNITRITE 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 501
2AC2SOFTWAREHIS A:100 , HIS A:135 , HIS A:306 , NO2 A:508 , HOH A:2476BINDING SITE FOR RESIDUE CU A 502
3AC3SOFTWARETHR A:228 , GLY A:229 , HIS A:319 , LYS A:321 , HOH A:2425 , HOH A:2466BINDING SITE FOR RESIDUE ACT A 505
4AC4SOFTWAREGLY A:225 , PHE A:312 , HIS A:319 , HOH A:2468 , HOH A:2469 , HOH A:2470 , HOH A:2471 , HOH A:2472 , HOH A:2473 , HOH A:2475BINDING SITE FOR RESIDUE ACT A 506
5AC5SOFTWAREASP A:98 , HIS A:100 , HIS A:135 , ILE A:257 , HIS A:306 , LEU A:308 , CU A:502 , HOH A:2174 , HOH A:2476 , HOH A:2477BINDING SITE FOR RESIDUE NO2 A 508
6AC6SOFTWARETRP A:265 , THR A:267 , GLY A:268 , LYS A:269 , ASN A:272 , GLN A:278 , HOH A:2376 , HOH A:2390 , HOH A:2478BINDING SITE FOR RESIDUE ACT A 511
7AC7SOFTWAREALA A:27 , HIS A:28 , ILE A:175 , ACT A:513 , HOH A:2479 , HOH A:2480BINDING SITE FOR RESIDUE ACT A 512
8AC8SOFTWAREGLN A:30 , ACT A:512 , HOH A:2266 , HOH A:2482 , HOH A:2483BINDING SITE FOR RESIDUE ACT A 513
9AC9SOFTWAREARG A:250 , ASP A:251 , ARG A:253 , ASN A:307 , GLU A:310 , HOH A:2368 , HOH A:2465BINDING SITE FOR RESIDUE MLI A 504

(-) SS Bonds  (0, 0)

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

(-) 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 2BWI)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BWI)

(-) 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:334
 aligned with NIR_ACHCY | P25006 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:334
                                    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       364       374    
            NIR_ACHCY    45 VDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM 378
               SCOP domains d2bwia1 A:7-166 Nitrite reductase, NIR                                                                                                                          d2bwia2 A:167-340 Nitrite reductase, NIR                                                                                                                                       SCOP domains
               CATH domains 2bwiA01 A:7-158 Cupredoxins -  blue copper proteins                                                                                                     2bwiA02 A:159-325 Cupredoxins -  blue copper proteins                                                                                                                  --------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhh...eeeeeee................eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bwi A   7 VDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVVKPASM 340
                                    16        26        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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BWI)

(-) 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 2nrd 2y1a 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 MOL_ID: 1; MOLECULE: NITRITE REDUCTASE; CHAIN : A, B, C; EC: 1.7.99.3; OTHER_DETAILS : PH 6.2 ("62")
1nib MOL_ID: 1; MOLECULE: NITRITE REDUCTASE; CHAIN : A, B, C; EC: 1.7.99.3; OTHER_DETAILS : PH 6.8 ("68")
1nic MOL_ID: 1; MOLECULE: NITRITE REDUCTASE; CHAIN : NULL; EC: 1.7.99.3; OTHER_DETAILS: PH 6.0 ("KP")
1nid MOL_ID: 1; MOLECULE: NITRITE REDUCTASE; CHAIN : NULL; EC: 1.7.99.3; OTHER_DETAILS: PH 5.4 ("NT1") NITRITE SOAKED
1nie MOL_ID: 1; MOLECULE: NITRITE REDUCTASE; CHAIN : NULL; EC: 1.7.99.3; OTHER_DETAILS: PH 5.0 ("PH5")
1nif MOL_ID: 1; MOLECULE: NITRITE REDUCTASE; CHAIN : NULL; EC: 1.7.99.3; OTHER_DETAILS: PH 5.4 ("T2D") TYPE II COPPER DEPLETED
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
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
2nrd MOL_ID: 1; MOLECULE: NITRITE REDUCTASE; CHAIN : NULL; EC: 1.7.99.3; OTHER_DETAILS: PH 5.4 ("HR")