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(-) Description

Title :  COMPLETELY OXIDIZED STRUCTURE OF COPPER NITRITE REDUCTASE FROM ALCALIGENES FAECALIS
 
Authors :  Y. Fukuda, K. M. Tse, M. Suzuki, K. Diederichs, K. Hirata, T. Nakane, M. S E. Nango, K. Tono, Y. Joti, T. Kameshima, C. Song, T. Hatsui, M. Yabashi O. Nureki, H. Matsumura, T. Inoue, S. Iwata, E. Mizohata
Date :  17 Mar 15  (Deposition) - 09 Mar 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Nitrite, Copper, Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Fukuda, K. M. Tse, T. Nakane, T. Nakatsu, M. Suzuki, M. Sugahara, S. Inoue, T. Masuda, F. Yumoto, N. Matsugaki, E. Nango, K. Tono, Y. Joti T. Kameshima, C. Song, T. Hatsui, M. Yabashi, O. Nureki, M. E. Murphy, T. Inoue, S. Iwata, E. Mizohata
Redox-Coupled Proton Transfer Mechanism In Nitrite Reductas Revealed By Femtosecond Crystallography
Proc. Natl. Acad. Sci. Usa V. 113 2928 2016
PubMed-ID: 26929369  |  Reference-DOI: 10.1073/PNAS.1517770113

(-) Compounds

Molecule 1 - COPPER-CONTAINING NITRITE REDUCTASE
    Chains: A, B, C
    EC Number: 1.7.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 40-376
    Gene: NIRK, NIR
    Organism Scientific: ALCALIGENES FAECALIS
    Organism Taxid: 511
    Synonym: CU-NIR

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2CU6Ligand/IonCOPPER (II) 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 401
2AC2SOFTWAREHIS A:100 , HIS A:135 , CL A:403 , HIS C:306binding site for residue CU A 402
3AC3SOFTWAREHIS A:135 , CU A:402 , ILE C:257 , HIS C:306binding site for residue CL A 403
4AC4SOFTWAREILE A:257 , HIS A:306 , HIS B:135 , CU B:402binding site for residue CL A 404
5AC5SOFTWAREHIS B:95 , CYS B:136 , HIS B:145 , MET B:150binding site for residue CU B 401
6AC6SOFTWAREHIS A:306 , CL A:404 , HIS B:100 , HIS B:135binding site for residue CU B 402
7AC7SOFTWAREILE B:257 , HIS B:306 , HIS C:135 , CU C:402binding site for residue CL B 403
8AC8SOFTWAREHIS C:95 , CYS C:136 , HIS C:145 , MET C:150binding site for residue CU C 401
9AC9SOFTWAREHIS B:306 , CL B:403 , HIS C:100 , HIS C:135binding site for residue CU C 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YSC)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Pro A:22 -Pro A:23
2Val A:68 -Pro A:69
3Pro B:22 -Pro B:23
4Val B:68 -Pro B:69
5Pro C:22 -Pro C:23
6Val C:68 -Pro C:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YSC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YSC)

(-) Exons   (0, 0)

(no "Exon" information available for 4YSC)

(-) 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:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhh..eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee................eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ysc A   4 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 339
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333      


Chain B from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhh........eeeeeeee....eeeeee.....hhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee...............hhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ysc B   4 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 339
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333      


Chain C from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ysc C   4 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPS 338
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333
   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  (0, 0)

(no "SCOP Domain" information available for 4YSC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YSC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YSC)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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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_ALCFA | P38501: 1aq8 1as6 1as7 1as8 1et5 1et7 1et8 1j9q 1j9r 1j9s 1j9t 1l9o 1l9p 1l9q 1l9r 1l9s 1l9t 1npj 1npn 1ntd 1sjm 1snr 1zdq 1zds 2afn 2b08 2e86 2fjs 2p80 2pp7 2pp8 2pp9 2ppa 2ppc 2ppd 2ppe 2ppf 3h4f 3h4h 3h56 4yse 5d4h 5d4i 5d4j 5f7a 5f7b

(-) Related Entries Specified in the PDB File

4ysa 4ysd 4yse 4yso 4ysp 4ysq 4ysr 4yss 4yst 4ysu