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(-) Description

Title :  CYTOCHROME CD1 NITRITE REDUCTASE, DIOXYGEN COMPLEX
 
Authors :  T. Sjogren, J. Hajdu
Date :  08 Jan 01  (Deposition) - 16 Jan 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Enzyme, Nitrite Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Sjogren, J. Hajdu
Structure Of The Bound Dioxygen Species In The Cytochrome Oxidase Reaction Of Cytochrome Cd1 Nitrite Reductase
J. Biol. Chem. V. 276 13072 2001
PubMed-ID: 11278884  |  Reference-DOI: 10.1074/JBC.M011312200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NITRITE REDUCTASE
    Cellular Location: PERIPLASM
    Chains: A, B
    Gene: NIRS
    Organism Scientific: PARACOCCUS PANTOTROPHUS
    Organism Taxid: 82367
    Other Details: ORGANISM FORMERLY KNOWN AS THIOSPHAERA PANTOTROPHA

 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
1DHE2Ligand/IonHEME D
2GOL2Ligand/IonGLYCEROL
3HEC2Ligand/IonHEME C
4OXY1Ligand/IonOXYGEN MOLECULE
5SO43Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:308 , ARG A:354 , LYS A:372BINDING SITE FOR RESIDUE SO4 A 621
02AC2SOFTWARETYR B:308 , ARG B:354 , LYS B:372 , HOH B:2279 , HOH B:2407BINDING SITE FOR RESIDUE SO4 B 621
03AC3SOFTWAREGLY B:439 , GLY B:440 , ASN B:461 , HOH B:2305 , HOH B:2315BINDING SITE FOR RESIDUE SO4 B 622
04AC4SOFTWAREHIS A:17 , ARG A:64 , CYS A:65 , CYS A:68 , HIS A:69 , GLY A:78 , LYS A:79 , LEU A:81 , LEU A:89 , TYR A:93 , LEU A:94 , PHE A:97 , SER A:102 , PRO A:103BINDING SITE FOR RESIDUE HEC A 601
05AC5SOFTWARETYR A:25 , PRO A:27 , SER A:28 , MET A:106 , ARG A:174 , HIS A:200 , ILE A:201 , ARG A:203 , ARG A:216 , ARG A:243 , SER A:244 , ILE A:245 , 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 , HOH A:2002 , HOH A:2189 , HOH A:2385 , HOH A:2386 , HOH A:2387BINDING SITE FOR RESIDUE DHE A 602
06AC6SOFTWAREARG B:64 , CYS B:65 , CYS B:68 , HIS B:69 , THR B:77 , GLY B:78 , LYS B:79 , TYR B:93 , LEU B:94 , PHE B:97 , ILE B:98 , ALA B:104 , GLY B:105 , MET B:106 , TRP B:109 , HOH B:2402BINDING SITE FOR RESIDUE HEC B 601
07AC7SOFTWAREPRO 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 , ILE B:245 , TYR B:263 , ALA B:302 , ILE B:303 , HIS B:345 , ARG B:391 , PHE B:444 , GLN B:507 , TRP B:522 , GLY B:555 , PHE B:557 , OXY B:603 , HOH B:2189 , HOH B:2403 , HOH B:2404 , HOH B:2405 , HOH B:2406BINDING SITE FOR RESIDUE DHE B 602
08AC8SOFTWAREHIS B:345 , HIS B:388 , DHE B:602BINDING SITE FOR RESIDUE OXY B 603
09AC9SOFTWAREPHE A:395 , VAL A:396 , PRO A:449 , SER A:451 , ILE A:475 , HOH A:2298 , HOH A:2388BINDING SITE FOR RESIDUE GOL A 611
10BC1SOFTWAREASP B:30 , ARG B:174 , TYR B:197BINDING SITE FOR RESIDUE GOL B 612

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HJ3)

(-) 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 1HJ3)

(-) 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 1HJ3)

(-) 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:544
 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 d1hj3a1 A:17-133 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase                                      d1hj3a2 A:134-567 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------------------1hj3A01 A:36-135 Cytochrome c                                                                       1hj3A02 A:136-566  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                         - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhh..............hhhhhhhhhhhhhhhh................hhhhhhhh.hhhhhhhhhh.......-------.hhhhhhhhhhhhhh.........hhhhhhhhee..hhhhh........hhhh.eeee......eeee......eeeee.......eeee.....eeeee.....eeeee.......eeeee.........ee..........eee......eeeee......eeeeee................eeeeee.....eeeeee.....eeeee.....eeeeeee................eeeeeehhhheeeeee.....eeeee.............ee.......eeeee.....eeeee......hhhhh....eeee........ee......eeee.............eeeee.hhh.........eeehhhhhh.......eee.........eeeeeee.......eeeeee....eeeeee...........eehhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------CYTC  PDB: A:52-131 UniProt: 81-160                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hj3 A  17 HKTRTDNRYEPSLDNLAQQDVAAPGAPEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYGSPAGMP-------LSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 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 
                                                                                                                    107     115                                                                                                                                                                                                                                                                                                                                                                                                                                                                    


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 d1hj3b1 B:26-133 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase                             d1hj3b2 B:134-567 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------1hj3B01 B:36-135 Cytochrome c                                                                       1hj3B02 B:136-567  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................hhhhhhhhhhhhhhhh................hhhhhhhh.hhhhhhhhhh...............hhhhhhhhhhhhhh.........hhhhhhhhee..hhhhh........hhhh.eeee......eeee......eeeee.......eeee.....eeeee.....eeeee.......eeeee.........ee..........eee......eeeee......eeeeee................eeeeee.....eeeeee.....eeeee.....eeeeeee................eeeeeehhh.eeeeee.....eeeeee............ee.......eeeee.....eeeee......hhhhh....eeee........ee......eeee.............eeeee.hhh.........eeehhhhhh.......eee.........eeeeeee.......eeeeee....eeeeee...........eehhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------CYTC  PDB: B:52-131 UniProt: 81-160                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hj3 B  26 EPSLDNLAQQDVAAPGAPEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 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)
  - → 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 1HJ3)

(-) 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: 1aof 1aom 1aoq 1dy7 1e2r 1gq1 1h9x 1h9y 1hcm 1hj4 1hj5 1qks

(-) Related Entries Specified in the PDB File

1aof CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED FORM
1hj4 CYTOCHROME CD1 NITRITE REDUCTASE, X-RAY REDUCED DIOXYGEN COMPLEX
1hj5 CYTOCHROME CD1 NITRITE REDUCTASE, REOXIDISED ENZYME