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(-) Description

Title :  CRYSTAL STRUCTURE OF ELECTRON TRANSFER COMPLEX OF NITRITE REDUCTASE WITH CYTOCHROME C
 
Authors :  M. Nojiri, H. Koteishi, K. Yamaguchi, S. Suzuki
Date :  27 May 08  (Deposition) - 09 Jun 09  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,G
Keywords :  Nitrite, Electron Transfer, Denitrification, Oxidoreductase-Electron Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nojiri, H. Koteishi, T. Nakagami, K. Kobayashi, T. Inoue, K. Yamaguchi, S. Suzuki
Structural Basis Of Inter-Protein Electron Transfer For Nitrite Reduction In Denitrification
Nature V. 462 117 2009
PubMed-ID: 19890332  |  Reference-DOI: 10.1038/NATURE08507

(-) Compounds

Molecule 1 - DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
    Chains: A, B, C
    EC Number: 1.7.2.1
    Fragment: UNP RESIDUES 25-360
    Organism Common: ALCALIGENES XYLOSOXIDANS
    Organism Scientific: ACHROMOBACTER XYLOSOXIDANS
    Organism Taxid: 85698
    Strain: GIFU1051
    Synonym: NITRITE REDUCTASE (NIR)
 
Molecule 2 - CYTOCHROME C551
    Chains: G
    Organism Common: ALCALIGENES XYLOSOXIDANS
    Organism Scientific: ACHROMOBACTER XYLOSOXIDANS
    Organism Taxid: 85698
    Strain: GIFU1051

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1CU6Ligand/IonCOPPER (II) ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:89 , CYS A:130 , HIS A:139 , MET A:144BINDING SITE FOR RESIDUE CU A 400
2AC2SOFTWAREHIS A:94 , HIS A:129 , HIS B:300BINDING SITE FOR RESIDUE CU A 401
3AC3SOFTWAREHIS B:89 , CYS B:130 , HIS B:139 , MET B:144BINDING SITE FOR RESIDUE CU B 400
4AC4SOFTWAREHIS B:94 , HIS B:129 , HIS C:300BINDING SITE FOR RESIDUE CU B 401
5AC5SOFTWAREHIS C:89 , CYS C:130 , HIS C:139 , MET C:144BINDING SITE FOR RESIDUE CU C 400
6AC6SOFTWAREHIS A:300 , HIS C:94 , HIS C:129BINDING SITE FOR RESIDUE CU C 401
7AC7SOFTWAREMET A:87 , CYS G:20 , CYS G:23 , HIS G:24 , ALA G:29 , ALA G:31 , PHE G:43 , THR G:54 , LYS G:59 , ALA G:61 , MET G:62 , PRO G:63 , ARG G:65 , GLY G:66 , LEU G:75 , MET G:82BINDING SITE FOR RESIDUE HEM G 200

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Pro A:16 -Pro A:17
2Met A:62 -Pro A:63
3Pro B:16 -Pro B:17
4Met B:62 -Pro B:63
5Pro C:16 -Pro C:17
6Met C:62 -Pro C:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZON)

(-) Sequences/Alignments

Asymmetric/Biological 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 O68601_ALCXX | O68601 from UniProtKB/TrEMBL  Length:360

    Alignment length:334
                                    35        45        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    
         O68601_ALCXX    26 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIP 359
               SCOP domains d2zona1 A:2-159 Nitrite reductase, NIR                                                                                                                        d2zona2 A:160-335 Nitrite reductase, NIR                                                                                                                                         SCOP domains
               CATH domains 2zonA01 A:2-152 Cupredoxins -  blue copper proteins                                                                                                    2zonA02 A:153-319 Cupredoxins -  blue copper proteins                                                                                                                  ---------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee....ee.....ee...eeeeeeeeee...............hhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eee....eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zon A   2 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIP 335
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331    


Chain B from PDB  Type:PROTEIN  Length:334
 aligned with O68601_ALCXX | O68601 from UniProtKB/TrEMBL  Length:360

    Alignment length:334
                                    35        45        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    
         O68601_ALCXX    26 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIP 359
               SCOP domains d2zonb1 B:2-159 Nitrite reductase, NIR                                                                                                                        d2zonb2 B:160-335 Nitrite reductase, NIR                                                                                                                                         SCOP domains
               CATH domains 2zonB01 B:2-152 Cupredoxins -  blue copper proteins                                                                                                    2zonB02 B:153-319 Cupredoxins -  blue copper proteins                                                                                                                  ---------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eee....eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zon B   2 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIP 335
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331    


Chain C from PDB  Type:PROTEIN  Length:334
 aligned with O68601_ALCXX | O68601 from UniProtKB/TrEMBL  Length:360

    Alignment length:334
                                    35        45        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    
         O68601_ALCXX    26 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIP 359
               SCOP domains d2zonc1 C:2-159 Nitrite reductase, NIR                                                                                                                        d2zonc2 C:160-335 Nitrite reductase, NIR                                                                                                                                         SCOP domains
               CATH domains 2zonC01 C:2-152 Cupredoxins -  blue copper proteins                                                                                                    2zonC02 C:153-319 Cupredoxins -  blue copper proteins                                                                                                                  ---------------- CATH domains
           Pfam domains (1) ------------------------------------Cu-oxidase_3-2zonC04 C:38-155                                                                                         ------------Cu-oxidase-2zonC01 C:168-320                                                                                                                             --------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------Cu-oxidase_3-2zonC05 C:38-155                                                                                         ------------Cu-oxidase-2zonC02 C:168-320                                                                                                                             --------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------Cu-oxidase_3-2zonC06 C:38-155                                                                                         ------------Cu-oxidase-2zonC03 C:168-320                                                                                                                             --------------- Pfam domains (3)
         Sec.struct. author ......eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zon C   2 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIP 335
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331    


Chain G from PDB  Type:PROTEIN  Length:81
 aligned with D0VWQ8_ALCXX | D0VWQ8 from UniProtKB/TrEMBL  Length:87

    Alignment length:81
                                    16        26        36        46        56        66        76        86 
         D0VWQ8_ALCXX     7 QLDPAGEKLYRSACVVCHASGVANAPKLGDKQAWAPFLAQGADALLATVLKGKGAMPPRGGTAADEATLRAAVAYMMDAAR  87
               SCOP domains d2zong_ G: automated matches                                                      SCOP domains
               CATH domains 2zonG00 G:7-87 Cytochrome c                                                       CATH domains
               Pfam domains Cytochrome_CBB3-2zonG01 G:7-82                                              ----- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh.hhhhh....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 2zon G   7 QLDPAGEKLYRSACVVCHASGVANAPKLGDKQAWAPFLAQGADALLATVLKGKGAMPPRGGTAADEATLRAAVAYMMDAAR  87
                                    16        26        36        46        56        66        76        86
   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  (2, 7)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 7)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 7)

Asymmetric/Biological Unit
(-)
Clan: CU_oxidase (192)
(-)
Clan: Cytochrome-c (108)

(-) Gene Ontology  (9, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (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.

Chain G   (D0VWQ8_ALCXX | D0VWQ8)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  2zon
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  O68601_ALCXX | O68601
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  1.7.2.1
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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 2vn3 2vw4 2vw6 2vw7 2xwz 2xx0 2xx1 2xxf 2xxg 4csp 4csz 5b1j 5b1k

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2ZON)