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(-) Description

Title :  REDUCED MUTANT D98N OF AFNIR EXPOSED TO NITRIC OXIDE
 
Authors :  E. I. Tocheva, M. E. P. Murphy
Date :  28 Apr 07  (Deposition) - 15 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Nitrite Reductase, D98N, Nitric Oxide, Denitrification, Bacteria, 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
    Mutation: YES
    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, 21)

Asymmetric/Biological Unit (5, 21)
No.NameCountTypeFull Name
1ACT8Ligand/IonACETATE ION
3CU3Ligand/IonCOPPER (II) ION
2CU15Ligand/IonCOPPER (I) ION
4NO4Ligand/IonNITRIC OXIDE
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
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 , NO A:1511 , HIS B:306BINDING SITE FOR RESIDUE CU A 502
03AC3SOFTWAREHIS B:95 , CYS B:136 , HIS B:145 , MET B:150 , CU1 B:504BINDING SITE FOR RESIDUE CU1 B 501
04AC4SOFTWAREHIS B:100 , HIS B:135 , NO B:503 , HIS C:306BINDING SITE FOR RESIDUE CU B 502
05AC5SOFTWAREHIS C:95 , CYS C:136 , HIS C:145 , MET C:150 , CU1 C:504BINDING SITE FOR RESIDUE CU1 C 501
06AC6SOFTWAREHIS A:306 , NO A:503 , HIS C:100 , HIS C:135 , NO C:505BINDING SITE FOR RESIDUE CU C 502
07AC7SOFTWARECYS B:136 , PRO B:138 , HIS B:145 , CU1 B:501BINDING SITE FOR RESIDUE CU1 B 504
08AC8SOFTWARECYS C:136 , PRO C:138 , HIS C:145 , CU1 C:501BINDING SITE FOR RESIDUE CU1 C 504
09AC9SOFTWARETHR B:228 , GLY B:229 , HIS B:319 , HOH B:1829BINDING SITE FOR RESIDUE ACT B 1503
10BC1SOFTWAREGLU A:113 , HOH A:1547 , 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
12BC3SOFTWAREHOH A:1670 , PHE B:282 , HOH B:1516 , HOH B:1678 , HOH B:1681 , PHE C:282 , HOH C:1643BINDING SITE FOR RESIDUE ACT B 1506
13BC4SOFTWAREVAL C:59 , HIS C:60 , TYR C:184 , THR C:206 , HOH C:1539 , HOH C:1623 , HOH C:1630BINDING SITE FOR RESIDUE ACT C 1507
14BC5SOFTWAREGLU A:313 , GLY C:140 , MET C:141 , VAL C:142 , PRO C:143 , TRP C:144BINDING SITE FOR RESIDUE ACT C 1508
15BC6SOFTWARETHR C:228 , GLY C:229 , ILE C:300 , HIS C:319 , LYS C:321BINDING SITE FOR RESIDUE ACT C 1509
16BC7SOFTWAREGLY A:140 , MET A:141 , VAL A:142 , PRO A:143 , TRP A:144 , TYR A:203 , VAL A:207 , GLU B:313 , GLU B:325BINDING SITE FOR RESIDUE ACT A 1510
17BC8SOFTWAREILE A:257 , HIS A:306 , HIS C:135 , CU C:502 , NO C:505BINDING SITE FOR RESIDUE NO A 503
18BC9SOFTWAREILE A:257 , HIS A:306 , NO A:503 , HIS C:100 , HIS C:135 , CU C:502 , HOH C:1510BINDING SITE FOR RESIDUE NO C 505
19CC1SOFTWAREHIS A:100 , HIS A:135 , CU A:502 , HOH A:1512 , ILE B:257 , HIS B:306BINDING SITE FOR RESIDUE NO A 1511
20CC2SOFTWAREHIS B:100 , HIS B:135 , CU B:502 , HOH B:1849 , ILE C:257 , HIS C:306BINDING SITE FOR RESIDUE NO B 503
21CC3SOFTWARETHR A:212 , LEU A:213 , THR A:214 , THR B:212 , LEU B:213 , THR B:214 , HOH B:1513 , HOH B:1669 , THR C:212 , LEU C:213 , THR C:214BINDING SITE FOR RESIDUE TRS B 1501

(-) SS Bonds  (0, 0)

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

(-) 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 2PPF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PPF)

(-) 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 d2ppfa1 A:4-166 Nitrite reductase, NIR                                                                                                                             d2ppfa2 A:167-339 Nitrite reductase, NIR                                                                                                                                      SCOP domains
               CATH domains -------2ppfA01 A:11-158 Cupredoxins -  blue copper proteins                                                                                                2ppfA02 A: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.....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
                 2ppf A   4 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNINFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 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 d2ppfb1 B:4-166 Nitrite reductase, NIR                                                                                                                             d2ppfb2 B:167-340 Nitrite reductase, NIR                                                                                                                                       SCOP domains
               CATH domains -------2ppfB01 B:11-158 Cupredoxins -  blue copper proteins                                                                                                2ppfB02 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
                 2ppf B   4 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNINFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSGT 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 d2ppfc1 C:4-166 Nitrite reductase, NIR                                                                                                                             d2ppfc2 C:167-339 Nitrite reductase, NIR                                                                                                                                      SCOP domains
               CATH domains -------2ppfC01 C:11-158 Cupredoxins -  blue copper proteins                                                                                                2ppfC02 C:159-325 Cupredoxins -  blue copper proteins                                                                                                                  -------------- CATH domains
           Pfam domains (1) ----------------------------------------Cu-oxidase_3-2ppfC04 C:44-161                                                                                         ------------Cu-oxidase-2ppfC01 C:174-326                                                                                                                             ------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------Cu-oxidase_3-2ppfC05 C:44-161                                                                                         ------------Cu-oxidase-2ppfC02 C:174-326                                                                                                                             ------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------Cu-oxidase_3-2ppfC06 C:44-161                                                                                         ------------Cu-oxidase-2ppfC03 C:174-326                                                                                                                             ------------- Pfam domains (3)
         Sec.struct. author .hhhhhhh..eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhh...eeeeeee................eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ppf C   4 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNINFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 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  (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 2ppc 2ppd 2ppe 3h4f 3h4h 3h56 4ysc 4yse 5d4h 5d4i 5d4j 5f7a 5f7b

(-) Related Entries Specified in the PDB File

1j9r NITRITE SOAKED REDUCED D98N AFNIR