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(-) Description

Title :  CHLORIDE-BOUND FORM OF A COPPER NITRITE REDUCTASE FROM ALCALIGENES FAECALS
 
Authors :  Y. Fukuda, K. M. Tse, T. Nakane, T. Nakatsu, M. Suzuki, M. Sugahara, S. In F. Yumoto, N. Matsugaki, E. Nango, K. Tono, Y. Joti, T. Kameshima, C. So M. Yabashi, O. Nureki, M. E. P. Murphy, T. Inoue, S. Iwata, E. Mizohata
Date :  07 Aug 15  (Deposition) - 09 Mar 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Copper, 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 BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    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  (4, 22)

Asymmetric/Biological Unit (4, 22)
No.NameCountTypeFull Name
1ACY3Ligand/IonACETIC ACID
2CL3Ligand/IonCHLORIDE ION
3CU6Ligand/IonCOPPER (II) ION
4GOL10Ligand/IonGLYCEROL

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:95 , CYS A:136 , HIS A:145 , MET A:150binding site for residue CU A 501
02AC2SOFTWAREHIS A:100 , HIS A:135 , HIS C:306 , CL C:601binding site for residue CU A 502
03AC3SOFTWAREILE A:257 , HIS A:306 , ASP B:98 , HIS B:135 , CU B:502binding site for residue CL A 503
04AC4SOFTWAREPHE A:24 , VAL A:25 , LYS A:174 , ILE A:175 , ACY A:507binding site for residue GOL A 504
05AC5SOFTWAREILE A:52 , ASP A:53 , ASP A:54 , ALA A:223 , VAL A:224 , HOH A:605 , HOH A:702binding site for residue GOL A 505
06AC6SOFTWARETYR A:193 , THR A:216 , HIS A:217 , GLU A:313 , LEU A:314 , ARG B:211binding site for residue GOL A 506
07AC7SOFTWAREHIS A:28 , GOL A:504 , HOH A:680binding site for residue ACY A 507
08AC8SOFTWAREHIS B:95 , CYS B:136 , HIS B:145 , MET B:150binding site for residue CU B 501
09AC9SOFTWAREHIS A:306 , CL A:503 , HIS B:100 , HIS B:135binding site for residue CU B 502
10AD1SOFTWAREILE B:257 , HIS B:306 , ASP C:98 , HIS C:135 , CU C:603binding site for residue CL B 503
11AD2SOFTWARETYR B:193 , THR B:216 , HIS B:217 , VAL B:224 , GLU B:313 , LEU B:314 , ARG C:211binding site for residue GOL B 504
12AD3SOFTWARETRP B:326 , THR B:332 , SER B:333binding site for residue GOL B 505
13AD4SOFTWAREGLU A:313 , GLY B:140 , MET B:141 , VAL B:142 , PRO B:143 , TRP B:144 , TYR B:203binding site for residue ACY B 506
14AD5SOFTWAREASP A:98 , HIS A:100 , HIS A:135 , CU A:502 , HIS C:255 , ILE C:257 , HIS C:306binding site for residue CL C 601
15AD6SOFTWAREHIS C:95 , CYS C:136 , HIS C:145 , MET C:150binding site for residue CU C 602
16AD7SOFTWAREHIS B:306 , CL B:503 , HIS C:100 , HIS C:135binding site for residue CU C 603
17AD8SOFTWARELEU A:106 , ALA A:137 , ALA C:302 , HOH C:707 , HOH C:738binding site for residue GOL C 604
18AD9SOFTWARETRP C:326 , ASP C:328 , THR C:332 , SER C:333binding site for residue GOL C 605
19AE1SOFTWARELEU A:213 , THR A:214 , LEU B:213 , THR B:214 , THR C:212 , LEU C:213 , THR C:214 , HOH C:735 , HOH C:753binding site for residue GOL C 606
20AE2SOFTWAREGLY A:229 , ASP A:230 , ALA A:232 , LYS A:321 , VAL C:51 , ASP C:53 , ASP C:54 , HOH C:732binding site for residue GOL C 607
21AE3SOFTWAREVAL C:59 , HIS C:60 , SER C:148 , THR C:206 , HOH C:718binding site for residue GOL C 608
22AE4SOFTWAREHIS C:28 , GLN C:30binding site for residue ACY C 609

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D4J)

(-) 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 5D4J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D4J)

(-) Exons   (0, 0)

(no "Exon" information available for 5D4J)

(-) 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:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee.......eeeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhh...eeeeeee................eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d4j A   6 AAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSGT 340
                                    15        25        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     


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....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5d4j 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:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5d4j C   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
   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 5D4J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D4J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D4J)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        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 4ysc 4yse 5d4h 5d4i 5f7a 5f7b

(-) Related Entries Specified in the PDB File

5d4h 5d4i