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(-) Description

Title :  OXIDIZED WILD TYPE AFNIR EXPOSED TO NO (NITRITE BOUND)
 
Authors :  E. I. Tocheva, M. E. P. Murphy
Date :  28 Apr 07  (Deposition) - 01 Apr 08  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Nitrite Reductase, Nitric Oxide, Denitrification, Nitrite, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. I. Tocheva, F. I. Rosell, A. G. Mauk, M. E. Murphy
Stable Copper-Nitrosyl Formation By Nitrite Reductase In Either Oxidation State.
Biochemistry V. 46 12366 2007
PubMed-ID: 17924665  |  Reference-DOI: 10.1021/BI701205J

(-) 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 Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NIRK, NIR
    Organism Scientific: ALCALIGENES FAECALIS
    Organism Taxid: 511
    Strain: S-6
    Synonym: CU-NIR

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 20)

Asymmetric/Biological Unit (5, 20)
No.NameCountTypeFull Name
1ACT10Ligand/IonACETATE ION
3CU3Ligand/IonCOPPER (II) ION
2CU13Ligand/IonCOPPER (I) ION
4NO23Ligand/IonNITRITE ION
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:95 , CYS A:136 , HIS A:145 , MET A:150BINDING SITE FOR RESIDUE CU1 A 501
02AC2SOFTWAREHIS A:100 , HIS A:135 , NO2 A:503 , HIS B:306BINDING SITE FOR RESIDUE CU A 502
03AC3SOFTWAREASP A:98 , HIS A:100 , HIS A:135 , CU A:502 , HIS B:255 , ILE B:257 , HIS B:306 , LEU B:308BINDING SITE FOR RESIDUE NO2 A 503
04AC4SOFTWAREGLY A:140 , MET A:141 , VAL A:142 , PRO A:143 , TRP A:144 , TYR A:203 , VAL A:207 , MET A:210 , GLU B:313 , GLU B:325BINDING SITE FOR RESIDUE ACT A 1510
05AC5SOFTWAREHIS B:95 , CYS B:136 , HIS B:145 , MET B:150BINDING SITE FOR RESIDUE CU1 B 501
06AC6SOFTWAREHIS B:100 , HIS B:135 , NO2 B:503 , ACT B:504 , HIS C:306BINDING SITE FOR RESIDUE CU B 502
07AC7SOFTWAREASP B:98 , HIS B:100 , HIS B:135 , CU B:502 , ACT B:504 , HOH B:1799 , ILE C:257 , HIS C:306 , LEU C:308BINDING SITE FOR RESIDUE NO2 B 503
08AC8SOFTWAREASP B:98 , HIS B:100 , HIS B:135 , ALA B:137 , CU B:502 , NO2 B:503 , HOH B:1799 , ILE C:257 , HIS C:306BINDING SITE FOR RESIDUE ACT B 504
09AC9SOFTWARETHR B:228 , GLY B:229 , HIS B:319BINDING SITE FOR RESIDUE ACT B 1503
10BC1SOFTWAREGLU A:113 , HOH A:1545 , ASP B:173 , GLY B:238 , GLU B:239 , LYS B:240 , HOH B:1587BINDING SITE FOR RESIDUE ACT B 1504
11BC2SOFTWAREGLY B:140 , MET B:141 , VAL B:142 , PRO B:143 , TRP B:144 , MET B:210 , GLU C:313BINDING SITE FOR RESIDUE ACT B 1505
12BC3SOFTWAREPHE B:282 , HOH B:1515 , HOH B:1677 , HOH B:1682 , PHE C:282 , HOH C:1642BINDING SITE FOR RESIDUE ACT B 1506
13BC4SOFTWAREHIS C:95 , CYS C:136 , HIS C:145 , MET C:150BINDING SITE FOR RESIDUE CU1 C 501
14BC5SOFTWAREHIS A:306 , HIS C:100 , HIS C:135 , NO2 C:503 , ACT C:504BINDING SITE FOR RESIDUE CU C 502
15BC6SOFTWAREHIS A:255 , ILE A:257 , HIS A:306 , LEU A:308 , ASP C:98 , HIS C:100 , HIS C:135 , CU C:502 , ACT C:504 , HOH C:1753BINDING SITE FOR RESIDUE NO2 C 503
16BC7SOFTWAREILE A:257 , HIS A:306 , ASP C:98 , HIS C:100 , HIS C:135 , ALA C:137 , CU C:502 , NO2 C:503 , HOH C:1753BINDING SITE FOR RESIDUE ACT C 504
17BC8SOFTWAREVAL C:59 , HIS C:60 , TYR C:184 , THR C:206 , HOH C:1539 , HOH C:1622 , HOH C:1629BINDING SITE FOR RESIDUE ACT C 1507
18BC9SOFTWAREGLU A:313 , GLY C:140 , MET C:141 , VAL C:142 , PRO C:143 , TRP C:144 , MET C:210BINDING SITE FOR RESIDUE ACT C 1508
19CC1SOFTWARETHR C:228 , GLY C:229 , ILE C:300 , HIS C:319 , LYS C:321BINDING SITE FOR RESIDUE ACT C 1509
20CC2SOFTWARETHR A:212 , LEU A:213 , THR A:214 , HOH A:1660 , HOH A:1701 , HOH A:1708 , THR B:212 , LEU B:213 , THR B:214 , THR C:212 , LEU C:213 , THR C:214BINDING SITE FOR RESIDUE TRS A 1501

(-) SS Bonds  (0, 0)

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

(-) 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 2PPC)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PPC)

(-) 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
 aligned with NIR_ALCFA | P38501 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:336
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369      
            NIR_ALCFA    40 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 375
               SCOP domains d2ppca1 A:4-166 Nitrite reductase, NIR                                                                                                                             d2ppca2 A:167-339 Nitrite reductase, NIR                                                                                                                                      SCOP domains
               CATH domains -------2ppcA01 A:11-158 Cupredoxins -  blue copper proteins                                                                                                2ppcA02 A:159-325 Cupredoxins -  blue copper proteins                                                                                                                  -------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh.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.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ppc 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:337
 aligned with NIR_ALCFA | P38501 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:337
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       
            NIR_ALCFA    40 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSGT 376
               SCOP domains d2ppcb1 B:4-166 Nitrite reductase, NIR                                                                                                                             d2ppcb2 B:167-340 Nitrite reductase, NIR                                                                                                                                       SCOP domains
               CATH domains -------2ppcB01 B:11-158 Cupredoxins -  blue copper proteins                                                                                                2ppcB02 B:159-325 Cupredoxins -  blue copper proteins                                                                                                                  --------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...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
                 2ppc B   4 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSGT 340
                                    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
 aligned with NIR_ALCFA | P38501 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:336
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369      
            NIR_ALCFA    40 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 375
               SCOP domains d2ppcc1 C:4-166 Nitrite reductase, NIR                                                                                                                             d2ppcc2 C:167-339 Nitrite reductase, NIR                                                                                                                                      SCOP domains
               CATH domains -------2ppcC01 C:11-158 Cupredoxins -  blue copper proteins                                                                                                2ppcC02 C:159-325 Cupredoxins -  blue copper proteins                                                                                                                  -------------- CATH domains
           Pfam domains (1) ----------------------------------------Cu-oxidase_3-2ppcC04 C:44-161                                                                                         ------------Cu-oxidase-2ppcC01 C:174-326                                                                                                                             ------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------Cu-oxidase_3-2ppcC05 C:44-161                                                                                         ------------Cu-oxidase-2ppcC02 C:174-326                                                                                                                             ------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------Cu-oxidase_3-2ppcC06 C:44-161                                                                                         ------------Cu-oxidase-2ppcC03 C:174-326                                                                                                                             ------------- Pfam domains (3)
         Sec.struct. author .hhhhhhh..eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....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
                 2ppc 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)
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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  (1, 6)

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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Clan: CU_oxidase (192)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (NIR_ALCFA | P38501)
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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  NIR_ALCFA | P38501
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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 2ppd 2ppe 2ppf 3h4f 3h4h 3h56 4ysc 4yse 5d4h 5d4i 5d4j 5f7a 5f7b

(-) Related Entries Specified in the PDB File

1sjm OXIDIZED WILD TYPE AFNIR-NITRITE
1snr REDUCED WILD TYPE AFNIR-NO