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(-) Description

Title :  CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED FORM
 
Authors :  P. A. Williams, V. Fulop
Date :  02 Jul 97  (Deposition) - 15 Oct 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Enzyme, Nitrite Reductase, Oxidoreductase, Nitrate Assimilation (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  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1DHE2Ligand/IonHEME D
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3SO22Ligand/IonSULFUR DIOXIDE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:64 , CYS A:65 , CYS A:68 , HIS A:69 , THR A:77 , GLY A:78 , LYS A:79 , LEU A:81 , TYR A:93 , PHE A:97 , SER A:102 , ALA A:104 , GLY A:105 , MET A:106 , TRP A:109BINDING SITE FOR RESIDUE HEM A 601
02AC2SOFTWAREARG 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 , THR A:554 , PHE A:557 , SO2 A:603 , HOH A:613 , HOH A:622 , HOH A:641 , HOH A:644 , HOH A:734BINDING SITE FOR RESIDUE DHE A 602
03AC3SOFTWAREHIS A:345 , HIS A:388 , PHE A:444 , DHE A:602BINDING SITE FOR RESIDUE SO2 A 603
04AC4SOFTWAREARG B:64 , CYS B:65 , CYS B:68 , HIS B:69 , GLY B:78 , LYS B:79 , TYR B:93 , SER B:102 , ALA B:104 , MET B:106 , PRO B:107 , TRP B:109 , HOH B:880BINDING SITE FOR RESIDUE HEM B 601
05AC5SOFTWAREPRO B:27 , SER B:28 , 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 , THR B:554 , GLY B:555 , PHE B:557 , SO2 B:603 , HOH B:604 , HOH B:623 , HOH B:633 , HOH B:636 , HOH B:637 , HOH B:715 , HOH B:746 , HOH B:850BINDING SITE FOR RESIDUE DHE B 602
06AC6SOFTWAREHIS B:345 , HIS B:388 , PHE B:444 , DHE B:602BINDING SITE FOR RESIDUE SO2 B 603
07C1AUNKNOWNHEM A:601THE C HEM IS THE POINT OF ELECTRON ENTRY.
08C1BUNKNOWNHEM B:601THE C HEM IS THE POINT OF ELECTRON ENTRY.
09D1AUNKNOWNDHE A:602THE D HEM IS THE SITE OF CATALYTIC ACTIVITY.
10D1BUNKNOWNDHE B:602THE D HEM IS THE SITE OF CATALYTIC ACTIVITY.

(-) SS Bonds  (0, 0)

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

(-) 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 1AOF)

(-) 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 1AOF)

(-) 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:532
 aligned with NIRS_PARPN | P72181 from UniProtKB/Swiss-Prot  Length:596

    Alignment length:532
                                    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       544       554       564       574       584       594  
           NIRS_PARPN    65 DVAAPGAPEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 596
               SCOP domains d1aofa1 A:36-133 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase                   d1aofa2 A:134-567 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1aofA01 A:36-135 Cytochrome c                                                                       1aofA02 A:136-567  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhh.hhhh.............hhhhhhh.hhhhhhhhhh................hhhhhhhhhhhh..........hhhhhhh......hhh..........hhh.eeeeehhh.eeeee......eeeeee....eeeeee.....eeeeee...eeeeee......eeeeeee......eeee.........eeeee.....eeeeee.....eeeeee...................eee.....eeeeee....eeeeee........eeeee.......eee.....eeeeeehhh.eeeeee....eeeeeee...........eeeee...eeeeeee.....eeeeee............eeeeee................eeee.......hhhh..eeeeehhh.........eeee.hhhh........eee.........eeeeeee.......eeeeee....eeeeee..........eeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------CYTC  PDB: A:52-131 UniProt: 81-160                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1aof A  36 DVAAPGAPEGVTALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYASPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQMNDWDLENLFSVTLRDAGQIALIDGSTYEIKTVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLNNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 567
                                    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       545       555       565  


Chain B from PDB  Type:PROTEIN  Length:542
 aligned with NIRS_PARPN | P72181 from UniProtKB/Swiss-Prot  Length:596

    Alignment length:542
                                    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       544       554       564       574       584       594  
           NIRS_PARPN    55 EPSLDNLAQQDVAAPGAPEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 596
               SCOP domains d1aofb1 B:26-133 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase                             d1aofb2 B:134-567 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------1aofB01 B:36-135 Cytochrome c                                                                       1aofB02 B:136-567  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.................hhhhhhhhhhhhhh.hhhh.............hhhhhhh.hhhhhhhhhh................hhhhhhhhhhhh..........hhhhhhh......hhh..........hhh.eeeeehhh.eeeee......eeeeee....eeeeee.....eeeeee...eeeeee......eeeeeee......eeee.........eeeee.....eeeeee.....eeeeee...................eee.....eeeeee....eeeeee........eeeee.......eee.....eeeeeehhh.eeeeee....eeeeeee...........eeeee...eeeeeee.....eeeeee............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
                 1aof B  26 EPSLDNLAQQDVAAPGAPEGVTALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYASPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQMNDWDLENLFSVTLRDAGQIALIDGSTYEIKTVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLNNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 567
                                    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       545       555       565
   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  (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 1AOF)

(-) 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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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