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(-) Description

Title :  OXYDIZED NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA
 
Authors :  D. Nurizzo, M. Tegoni, C. Cambillau
Date :  17 Jun 97  (Deposition) - 03 Dec 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nitrite Reductase, Pseudomonas Aeruginosa, Hemoprotein, Denitrification, Domain Swapping (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Nurizzo, M. C. Silvestrini, M. Mathieu, F. Cutruzzola, D. Bourgeois, V. Fulop, J. Hajdu, M. Brunori, M. Tegoni, C. Cambillau
N-Terminal Arm Exchange Is Observed In The 2. 15 A Crystal Structure Of Oxidized Nitrite Reductase From Pseudomonas Aeruginosa.
Structure V. 5 1157 1997
PubMed-ID: 9331415  |  Reference-DOI: 10.1016/S0969-2126(97)00267-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NITRITE REDUCTASE
    Cellular Location: PERIPLASMIC SPACE
    Chains: A, B
    EC Number: 1.9.3.2
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Other Details: EACH SUB-UNIT (A, B) LINKING ONE PHOSPHATE ION AND ONE CHLORIDE ION
    Other Details - Source: NCTC 6750

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2DHE2Ligand/IonHEME D
3HEC2Ligand/IonHEME C
4OH2Ligand/IonHYDROXIDE ION
5PO42Ligand/IonPHOSPHATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:673 , HIS B:335 , HIS B:540 , HOH B:770BINDING SITE FOR RESIDUE PO4 A 604
02AC2SOFTWARESER A:265 , GLY B:268 , MET B:269BINDING SITE FOR RESIDUE CL A 605
03AC3SOFTWAREHIS A:369 , DHE A:602 , TYR B:10BINDING SITE FOR RESIDUE OH A 603
04AC4SOFTWAREHIS A:335 , HIS A:540 , HOH A:744 , HOH B:984BINDING SITE FOR RESIDUE PO4 B 604
05AC5SOFTWAREGLY A:268 , MET A:269 , SER B:265BINDING SITE FOR RESIDUE CL B 605
06AC6SOFTWARETYR A:10 , HIS B:369 , DHE B:602BINDING SITE FOR RESIDUE OH B 603
07AC7SOFTWAREARG A:46 , CYS A:47 , CYS A:50 , HIS A:51 , THR A:59 , LEU A:63 , ARG A:71 , LEU A:79 , THR A:84 , LEU A:86 , GLY A:87 , MET A:88 , PRO A:89 , TRP A:91 , HOH A:722 , HOH A:770 , HOH A:822 , HOH A:895 , GLU B:8BINDING SITE FOR RESIDUE HEC A 601
08AC8SOFTWAREARG A:156 , HIS A:182 , ILE A:183 , ARG A:185 , ARG A:198 , ARG A:225 , SER A:226 , TYR A:245 , ALA A:283 , ALA A:284 , ILE A:285 , HIS A:327 , ARG A:372 , PHE A:425 , GLN A:483 , GLY A:531 , PHE A:533 , OH A:603 , HOH A:645 , HOH A:656 , HOH A:876 , HOH A:877 , HOH A:880 , HOH A:901 , HOH A:907 , HOH A:1010 , TYR B:10 , ALA B:13 , HOH B:884BINDING SITE FOR RESIDUE DHE A 602
09AC9SOFTWAREGLU A:8 , ARG B:46 , CYS B:47 , CYS B:50 , HIS B:51 , THR B:59 , LEU B:63 , ARG B:71 , LEU B:79 , THR B:84 , LEU B:86 , GLY B:87 , MET B:88 , PRO B:89 , TRP B:91 , HOH B:639 , HOH B:682 , HOH B:725 , HOH B:849BINDING SITE FOR RESIDUE HEC B 601
10BC1SOFTWARETYR A:10 , ARG B:156 , HIS B:182 , ARG B:185 , ARG B:198 , ARG B:225 , SER B:226 , TYR B:245 , ALA B:284 , ILE B:285 , HIS B:327 , ARG B:372 , PHE B:425 , PHE B:441 , GLN B:483 , GLY B:531 , PHE B:533 , OH B:603 , HOH B:609 , HOH B:640 , HOH B:662 , HOH B:711 , HOH B:863 , HOH B:872 , HOH B:890 , HOH B:891 , HOH B:980 , HOH B:981BINDING SITE FOR RESIDUE DHE B 602
11NIAUNKNOWNHIS A:327 , HIS A:369 , DHE A:602ACTIVE SITE.
12NIBUNKNOWNHIS B:327 , HIS B:369 , DHE B:602ACTIVE SITE.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:246 -Pro A:247
2Trp B:246 -Pro B:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NIR)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.NIRS_PSEAE59-138
 		  2A:34-113
B:34-113

(-) Exons   (0, 0)

(no "Exon" information available for 1NIR)

(-) 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:538
 aligned with NIRS_PSEAE | P24474 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:538
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560        
           NIRS_PSEAE    31 AAEQYQGAASAVDPAHVVRTNGAPDMSESEFNEAKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELSKEQITLMAKYIQHTPPQPPEWGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVKVIDTGYAVHISRMSASGRYLLVIGRDARIDMIDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMDGETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKVLLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSKDRRLSALVDVGKTPHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVFDLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSVWNGKNDSSALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDVY 568
               SCOP domains d1nira1 A:6-117 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase                                  d1nira2 A:118-543 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1nirA01 A:6-116 Cytochrome c                                                                                   1nirA02 A:117-543  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh........hhh...........hhhhhhhhhhhhhh.hhhh.............hhhhhhh.hhhhhhhhhh................hhhhhhhhhhhh..........hhhhhhh......hhh..........hhheeeeeehhh.eeeeee.....eeeeee....eeeeee.....eeeeee...eeeeee......eeeeeee......eeee.........eeeee.....eeeeee.....eeeeee...................eee.....eeeeee....eeeeee.......eeeeee.......eee.....eeeeeehhh.eeeeee....eeeeeee..........eeeee...eeeeeee.....eeeeee............eeeeee................eeee.......hhhh..eeeee........eee.hhhhh.......eee.........eeeeeee.......eeeeee....eeeeee..........eeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------CYTC  PDB: A:34-113 UniProt: 59-138                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nir A   6 AAEQYQGAASAVDPAHVVRTNGAPDMSESEFNEAKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELSKEQITLMAKYIQHTPPQPPEWGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVKVIDTGYAVHISRMSASGRYLLVIGRDARIDMIDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMDGETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKVLLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSKDRRLSALVDVGKTPHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVFDLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSVWNGKNDSSALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDVY 543
                                    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       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535        


Chain B from PDB  Type:PROTEIN  Length:539
 aligned with NIRS_PSEAE | P24474 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:539
                                    39        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       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559         
           NIRS_PSEAE    30 KAAEQYQGAASAVDPAHVVRTNGAPDMSESEFNEAKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELSKEQITLMAKYIQHTPPQPPEWGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVKVIDTGYAVHISRMSASGRYLLVIGRDARIDMIDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMDGETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKVLLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSKDRRLSALVDVGKTPHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVFDLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSVWNGKNDSSALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDVY 568
               SCOP domains d1nirb1 B:5-117 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase                                   d1nirb2 B:118-543 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -1nirB01 B:6-116 Cytochrome c                                                                                   1nirB02 B:117-543  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) -----------------------------Cytochrome_CBB3-1nirB03 B:34-109                                            ----------------------------------Cytochrom_D1-1nirB01 B:144-538                                                                                                                                                                                                                                                                                                                                                                             ----- Pfam domains (1)
           Pfam domains (2) -----------------------------Cytochrome_CBB3-1nirB04 B:34-109                                            ----------------------------------Cytochrom_D1-1nirB02 B:144-538                                                                                                                                                                                                                                                                                                                                                                             ----- Pfam domains (2)
         Sec.struct. author .hhhhh........hhh...........hhhhhhhhhhhhhh.hhhh.............hhhhhhh.hhhhhhhhhh................hhhhhhhhhhhh..........hhhhhhh...................hhheeeeeehhh.eeeeee.....eeeeee......eeee.....eeeee....eeeeee......eeeeeee......eeee.........eeeee.....eeeeee.....eeeeee...................eee.....eeeeee....eeeeee.......eeeeee.......eee.....eeeeeehhh.eeeeee....eeeeeee..........eeeee...eeeeeee.....eeeeee............eeeeee................eeee.......hhhh..eeeee........eee.hhhhh.......eee.........eeeeeee.......eeeeee....eeeeee..........eeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------CYTC  PDB: B:34-113 UniProt: 59-138                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nir B   5 KAAEQYQGAASAVDPAHVVRTNGAPDMSESEFNEAKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELSKEQITLMAKYIQHTPPQPPEWGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVKVIDTGYAVHISRMSASGRYLLVIGRDARIDMIDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMDGETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKVLLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSKDRRLSALVDVGKTPHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVFDLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSVWNGKNDSSALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDVY 543
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Beta_propeller (192)
(-)
Clan: Cytochrome-c (108)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NIRS_PSEAE | P24474)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0050418    hydroxylamine reductase activity    Catalysis of the reaction: NH3 + H2O + acceptor = hydroxylamine + reduced acceptor.
    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: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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NIRS_PSEAE | P24474: 1bl9 1gjq 1hzu 1hzv 1n15 1n50 1n90 1nno

(-) Related Entries Specified in the PDB File

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