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(-) Description

Title :  CRYSTAL STRUCTURE OF NITRITE SOAKED REDUCED D98N AFNIR
 
Authors :  M. J. Boulanger, M. E. Murphy
Date :  28 May 01  (Deposition) - 06 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Curpredoxin Fold Copper Nitrite, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Boulanger, M. E. Murphy
Alternate Substrate Binding Modes To Two Mutant (D98N And H255N) Forms Of Nitrite Reductase From Alcaligenes Faecalis S-6: Structural Model Of A Transient Catalytic Intermediate
Biochemistry V. 40 9132 2001
PubMed-ID: 11478880  |  Reference-DOI: 10.1021/BI0107400
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COPPER-CONTAINING NITRITE REDUCTASE
    Chains: A, B, C
    EC Number: 1.7.99.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: HMS174 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 40-376
    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  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1CU9Ligand/IonCOPPER (II) ION
2NO23Ligand/IonNITRITE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:95 , CYS A:136 , PRO A:138 , HIS A:145 , CU A:601BINDING SITE FOR RESIDUE CU A 600
02AC2SOFTWAREHIS A:95 , CYS A:136 , HIS A:145 , MET A:150 , CU A:600BINDING SITE FOR RESIDUE CU A 601
03AC3SOFTWAREHIS A:100 , HIS A:135 , NO2 A:604 , HIS B:306BINDING SITE FOR RESIDUE CU A 602
04AC4SOFTWAREASN A:98 , HIS A:100 , HIS A:135 , CU A:602 , HIS B:255 , ILE B:257 , HIS B:306BINDING SITE FOR RESIDUE NO2 A 604
05AC5SOFTWARECYS B:136 , PRO B:138 , HIS B:145 , CU B:701BINDING SITE FOR RESIDUE CU B 700
06AC6SOFTWAREHIS B:95 , CYS B:136 , HIS B:145 , MET B:150 , CU B:700BINDING SITE FOR RESIDUE CU B 701
07AC7SOFTWAREHIS B:100 , HIS B:135 , NO2 B:704 , HIS C:306BINDING SITE FOR RESIDUE CU B 702
08AC8SOFTWAREASN B:98 , HIS B:100 , HIS B:135 , CU B:702 , HIS C:255 , ILE C:257 , HIS C:306BINDING SITE FOR RESIDUE NO2 B 704
09AC9SOFTWARECYS C:136 , PRO C:138 , HIS C:145 , CU C:801BINDING SITE FOR RESIDUE CU C 800
10BC1SOFTWAREHIS C:95 , CYS C:136 , HIS C:145 , MET C:150 , CU C:800BINDING SITE FOR RESIDUE CU C 801
11BC2SOFTWAREHIS A:306 , HIS C:100 , HIS C:135 , NO2 C:804BINDING SITE FOR RESIDUE CU C 802
12BC3SOFTWAREILE A:257 , HIS A:306 , ASN C:98 , HIS C:100 , HIS C:135 , CU C:802BINDING SITE FOR RESIDUE NO2 C 804

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J9R)

(-) 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 1J9R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J9R)

(-) Exons   (0, 0)

(no "Exon" information available for 1J9R)

(-) 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 d1j9ra1 A:4-166 Nitrite reductase, NIR                                                                                                                             d1j9ra2 A:167-339 Nitrite reductase, NIR                                                                                                                                      SCOP domains
               CATH domains -------1j9rA01 A:11-158 Cupredoxins -  blue copper proteins                                                                                                1j9rA02 A:159-325 Cupredoxins -  blue copper proteins                                                                                                                  -------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee.......eeeee...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
                 1j9r 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: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 d1j9rb1 B:4-166 Nitrite reductase, NIR                                                                                                                             d1j9rb2 B:167-339 Nitrite reductase, NIR                                                                                                                                      SCOP domains
               CATH domains -------1j9rB01 B:11-158 Cupredoxins -  blue copper proteins                                                                                                1j9rB02 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..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j9r B   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 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 d1j9rc1 C:4-166 Nitrite reductase, NIR                                                                                                                             d1j9rc2 C:167-339 Nitrite reductase, NIR                                                                                                                                      SCOP domains
               CATH domains -------1j9rC01 C:11-158 Cupredoxins -  blue copper proteins                                                                                                1j9rC02 C:159-325 Cupredoxins -  blue copper proteins                                                                                                                  -------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhh..eee.....................eeeeeeeeeeeeee......eeeeeee.......eeeee...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
                 1j9r 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  (0, 0)

(no "Pfam Domain" information available for 1J9R)

(-) 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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  1j9r
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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 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 5d4j 5f7a 5f7b

(-) Related Entries Specified in the PDB File

1j9q CRYSTAL STRUCTURE OF NITRITE SOAKED OXIDIZED D98N AFNIR
1j9s CRYSTAL STRUCTURE OF NITRITE SOAKED OXIDIZED H255N AFNIR
1j9t CRYSTAL STRUCTURE OF NITRITE SOAKED REDUCED H255N AFNIR