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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ELECTRON-TRANSFER COMPLEX OF COPPER NITRITE REDUCTASE WITH A CUPREDOXIN
 
Authors :  M. Nojiri, H. Koteishi, R. Yoneda, D. Hira
Date :  04 Dec 15  (Deposition) - 23 Nov 16  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Complex, Copper Nitrite Reductase, Electron Transfer, Oxidoreductase- Electron Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nojiri
Structure And Function Of Copper Nitrite Reductase
Metalloenzymes In 91 2016 Denitrification: Applications And Environmental Impacts
PubMed: search  |  Reference-DOI: 10.1039/9781782623762-00091

(-) Compounds

Molecule 1 - COPPER-CONTAINING NITRITE REDUCTASE
    Chains: A, B
    EC Number: 1.7.2.1
    Fragment: UNP RESIDUES 25-360
    Organism Common: ACHROMOBACTER XYLOSOXIDANS
    Organism Scientific: ALCALIGENES XYLOSOXYDANS XYLOSOXYDANS
    Organism Taxid: 85698
    Synonym: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE,NITRITE REDUCTASE (NIR)
 
Molecule 2 - BLUE COPPER PROTEIN
    Chains: C
    Organism Scientific: HYPHOMICROBIUM DENITRIFICANS
    Organism Taxid: 53399
    Synonym: PSEUDOAZURIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1CU5Ligand/IonCOPPER (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:89 , CYS A:130 , HIS A:139 , MET A:144binding site for residue CU A 500
2AC2SOFTWAREASP A:92 , HIS A:94 , HIS A:129 , HIS A:249 , HIS A:300binding site for residue CU A 501
3AC3SOFTWAREHIS B:89 , CYS B:130 , HIS B:139 , MET B:144binding site for residue CU B 500
4AC4SOFTWAREASP B:92 , HIS B:94 , HIS B:129 , HIS B:300binding site for residue CU B 501
5AC5SOFTWAREHIS C:41 , CYS C:79 , HIS C:82 , MET C:87binding site for residue CU C 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B1J)

(-) Cis Peptide Bonds  (5, 5)

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
5Gln C:20 -Pro C:21

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B1J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B1J)

(-) Exons   (0, 0)

(no "Exon" information available for 5B1J)

(-) 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
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......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.................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b1j 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
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee.....eeeeeee...eeeeeeee..........ee....hhhhhhhhhh....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee....ee.....ee...eeeeeeeeee...............hhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eee....eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b1j 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:124
                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....eeeee..eeee....eeeee......eeee............eeee...eeee.....eeeee.hhhhhhh.eeeeee....hhhhhhhh...hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b1j C   1 AEHIVEMRNKDDAGNTMVFQPGFVKVEAGDTVKFVPTDKSHNAESVREVWPEGVAPVKGGFSKEVVFNAEKEGLYVLKCAPHYGMGMVVLVQVGKPVNLDQIKEYKATGLAKKRLDGEIAKVVQ 124
                                    10        20        30        40        50        60        70        80        90       100       110       120
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 5B1J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B1J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B1J)

(-) Gene Ontology  (7, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        A7VL37_9RHIZ | A7VL37: 3ef4
        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 2zon 4csp 4csz 5b1k

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5b1k