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(-) Description

Title :  CYTOCHROME CD1 NITRITE REDUCTASE WITH SUBSTRATE AND PRODUCT BOUND
 
Authors :  P. A. Williams, V. Fulop
Date :  09 Jul 97  (Deposition) - 04 Feb 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Enzyme, Nitrite Reductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. A. Williams, V. Fulop, E. F. Garman, N. F. Saunders, S. J. Ferguson, J. Hajdu
Haem-Ligand Switching During Catalysis In Crystals Of A Nitrogen-Cycle Enzyme.
Nature V. 389 406 1997
PubMed-ID: 9311786  |  Reference-DOI: 10.1038/38775
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NITRITE REDUCTASE
    Cellular Location: PERIPLASM
    Chains: A, B
    Organism Scientific: PARACOCCUS PANTOTROPHUS
    Organism Taxid: 82367

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
12NO1Ligand/IonNITROGEN DIOXIDE
2DHE2Ligand/IonHEME D
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4NO1Ligand/IonNITRIC OXIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:17 , ASN A:23 , ARG A:64 , CYS A:65 , CYS A:68 , HIS A:69 , GLY A:78 , LYS A:79 , LEU A:89 , TYR A:93 , LEU A:94 , PHE A:97 , SER A:102 , PRO A:103BINDING SITE FOR RESIDUE HEM A 601
2AC2SOFTWARETYR A:25 , PRO A:27 , SER A:28 , MET A:106 , TRP A:109 , ARG A:174 , HIS A:200 , ILE A:201 , ARG A:203 , ARG A:216 , ARG A:243 , SER A:244 , TYR A:263 , ALA A:302 , ILE A:303 , HIS A:345 , ARG A:391 , PHE A:444 , GLN A:507 , TRP A:522 , THR A:554 , GLY A:555 , PHE A:557 , 2NO A:603 , HOH A:613 , HOH A:637 , HOH A:719 , HOH A:835 , HOH A:870 , HOH A:974BINDING SITE FOR RESIDUE DHE A 602
3AC3SOFTWAREHIS A:345 , HIS A:388 , DHE A:602BINDING SITE FOR RESIDUE 2NO A 603
4AC4SOFTWAREASP B:16 , HIS B:17 , ASN B:23 , ARG B:64 , CYS B:65 , CYS B:68 , HIS B:69 , GLY B:78 , LYS B:79 , LEU B:81 , LEU B:89 , TYR B:93 , LEU B:94 , PHE B:97 , SER B:102 , PRO B:103 , HOH B:885 , HOH B:914 , HOH B:1011BINDING SITE FOR RESIDUE HEM B 601
5AC5SOFTWARETYR B:25 , PRO B:27 , SER B:28 , MET B:106 , TRP B:109 , ARG B:174 , HIS B:200 , ILE B:201 , ARG B:203 , ARG B:216 , ARG B:243 , SER B:244 , TYR B:263 , ALA B:302 , ILE B:303 , HIS B:345 , ARG B:391 , PHE B:444 , GLN B:507 , TRP B:522 , THR B:554 , GLY B:555 , PHE B:557 , NO B:603 , HOH B:630 , HOH B:735 , HOH B:737 , HOH B:769 , HOH B:798 , HOH B:907 , HOH B:962BINDING SITE FOR RESIDUE DHE B 602
6AC6SOFTWAREHIS B:345 , HIS B:388 , DHE B:602BINDING SITE FOR RESIDUE NO B 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:264 -Pro A:265
2Trp B:264 -Pro B:265

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.NIRS_PARPN81-160
 		  2A:52-131
B:52-131

(-) Exons   (0, 0)

(no "Exon" information available for 1AOQ)

(-) 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:551
 aligned with NIRS_PARPN | P72181 from UniProtKB/Swiss-Prot  Length:596

    Alignment length:551
                                    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       545       555       565       575       585       595 
           NIRS_PARPN    46 HKTRTDNRYEPSLDNLAQQDVAAPGAPEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 596
               SCOP domains d1aoqa1 A:17-133 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase                                      d1aoqa2 A:134-567 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------1aoqA01 A:36-135 Cytochrome c                                                                       1aoqA02 A:136-567  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhh................hhhhhhhhhhhhhh.hhhh.............hhhhhhh.hhhhhhhhhh................hhhhhhhhhhhh..........hhhhhhh......hhh..........hhheeeeeehhh.eeeeee.....eeeeee....eeeeee.....eeeeee...eeeeee.......eeeeee......eeee.........eeeeee....eeeeee.....eeeeee...................eee.....eeeeee....eeeeee........eeeee.......eee.....eeeeeehhh.eeeeee....eeeeeee...........eeeee...eeeeeee.....eeeeee............eeeeee................eeeee......hhhh..eeeeehhh.........eeee.hhhhh.......eee.........eeeeeee.......eeeeee....eeeeee..........eeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------CYTC  PDB: A:52-131 UniProt: 81-160                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1aoq A  17 HKTRTDNRYEPSLDNLAQQDVAAPGAPEGVTALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYASPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQMNDWDLENLFSVTLRDAGQIALIDGSTYEIKTVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLNNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 567
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566 


Chain B from PDB  Type:PROTEIN  Length:559
 aligned with NIRS_PARPN | P72181 from UniProtKB/Swiss-Prot  Length:596

    Alignment length:559
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587         
           NIRS_PARPN    38 DPAAALEDHKTRTDNRYEPSLDNLAQQDVAAPGAPEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 596
               SCOP domains d1aoqb1 B:9-133 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase                                               d1aoqb2 B:134-567 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------1aoqB01 B:36-135 Cytochrome c                                                                       1aoqB02 B:136-567  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh...............hhh................hhhhhhhhhhhhhh.hhhh.............hhhhhhh.hhhhhhhhhh................hhhhhhhhhhhh..........hhhhhhh......hhh..........hhh.eeeee....eeeee......eeeeee....eeeeee.....eeeeee...eeeeee.......eeeeee......eeee.........eeeeee....eeeeee.....eeeeee...................eee.....eeeeee....eeeeee........eeeee.......eee.....eeeeeehhh.eeeeee....eeeeeee...........eeeee...eeeeeee.....eeeeee......hhh...eeeeee................eeee.......hhhh..eeeeehhh.........eeee.hhhhh.......eee.........eeeeeee.......eeeeee....eeeeee..........eeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------CYTC  PDB: B:52-131 UniProt: 81-160                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1aoq B   9 DPAAALEDHKTRTDNRYEPSLDNLAQQDVAAPGAPEGVTALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYASPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQMNDWDLENLFSVTLRDAGQIALIDGSTYEIKTVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLNNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 567
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558
   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  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NIRS_PARPN | P72181)
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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  1aoq
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 Related Entries

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

UniProtKB/Swiss-Prot
        NIRS_PARPN | P72181: 1aof 1aom 1dy7 1e2r 1gq1 1h9x 1h9y 1hcm 1hj3 1hj4 1hj5 1qks

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1AOQ)