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(-) Description

Title :  CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED AND CYANIDE BOUND
 
Authors :  V. Fulop
Date :  24 May 00  (Deposition) - 30 May 00  (Release) - 19 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Denitrification, Electron Transport, Periplasmic, Cyanide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Jafferji, J. W. Allen, S. J. Ferguson, V. Fulop
X-Ray Crystallographic Study Of Cyanide Binding Provides Insights Into The Structure-Function Relationship For Cytochrome Cd1 Nitrite Reductase From Paracoccus Pantotrophus.
J. Biol. Chem. V. 275 25089 2000
PubMed-ID: 10827177  |  Reference-DOI: 10.1074/JBC.M001377200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NITRITE REDUCTASE
    Cellular Location: PERIPLASM
    Chains: A, B
    EC Number: 1.7.2.1, 1.7.99.1
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 266
    Other Details: SUBSP. PARACOCCUS PANTOTROPHUS FORMALLY KNOWN AS THIOSPHAERA PANTOTROPHA
    Synonym: CYTOCHROME CD1, CYTOCHROME OXIDASE, HYDROXYLAMINE REDUCTASE, CYTOCHROME CD1 NITRITE REDUCTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1CYN2Ligand/IonCYANIDE ION
2DHE2Ligand/IonHEME D
3GOL2Ligand/IonGLYCEROL
4HEC2Ligand/IonHEME C

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG 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:301 , ALA A:302 , ILE A:303 , HIS A:345 , ARG A:391 , PHE A:444 , GLN A:507 , PHE A:557 , CYN A:603 , HOH A:2236 , HOH A:2297 , HOH A:2642 , HOH A:2643 , HOH A:2644 , HOH A:2645 , HOH A:2646 , HOH A:2647 , HOH A:2648 , HOH A:2649BINDING SITE FOR RESIDUE DHE A 602
2AC2SOFTWARETYR B:25 , GLU B:26 , PRO 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:301 , 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 , CYN B:603 , GOL B:614 , HOH B:2302 , HOH B:2408 , HOH B:2685 , HOH B:2686 , HOH B:2687BINDING SITE FOR RESIDUE DHE B 602
3AC3SOFTWAREPHE A:395 , VAL A:396 , PRO A:449 , SER A:451 , ILE A:475 , HOH A:2517 , HOH A:2651 , HOH A:2652 , HOH A:2653BINDING SITE FOR RESIDUE GOL A 613
4AC4SOFTWARETYR B:25 , LYS B:317 , HIS B:345 , ASN B:361 , HIS B:388 , DHE B:602 , HOH B:2001 , HOH B:2417 , HOH B:2689 , HOH B:2690BINDING SITE FOR RESIDUE GOL B 614
5AC5SOFTWAREARG A:64 , CYS A:65 , CYS A:68 , HIS A:69 , THR A:77 , LEU A:89 , TYR A:93 , PHE A:97 , SER A:102 , ALA A:104 , GLY A:105 , MET A:106 , PRO A:107 , TRP A:109 , LEU A:115 , HOH A:2641BINDING SITE FOR RESIDUE HEC A 601
6AC6SOFTWAREARG B:64 , CYS B:65 , CYS B:68 , HIS B:69 , THR B:77 , GLY B:78 , LEU B:89 , TYR B:93 , LEU B:94 , PHE B:97 , SER B:102 , ALA B:104 , GLY B:105 , MET B:106 , PRO B:107 , TRP B:109 , LEU B:115 , HOH B:2077 , HOH B:2684BINDING SITE FOR RESIDUE HEC B 601
7AC7SOFTWAREHIS A:345 , HIS A:388 , DHE A:602BINDING SITE FOR RESIDUE CYN A 603
8AC8SOFTWARETYR B:25 , HIS B:345 , HIS B:388 , DHE B:602BINDING SITE FOR RESIDUE CYN B 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E2R)

(-) 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 1E2R)

(-) 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 1E2R)

(-) 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 d1e2ra1 A:36-135 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase                     d1e2ra2 A:136-567 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1e2rA01 A:36-135 Cytochrome c                                                                       1e2rA02 A:136-567  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh......hhhhhh..hhhhhhhhhhhhhh........hhhhhhhhh....hhhhh........hhh.eeeeee....eeeeee.....eeeeee....eeeeee.....eeeeee...eeeeee.......eeeeee......eeee.........eeeeee....eeeeee.....eeeeee...................eee.....eeeeee....eeeeee........eeeee.......eee.....eeeeee....eeeeee....eeeeeee...........eeeee...eeeeeee.....eeeeee............eeeeee................eeeee.....hhhhhh.eeeee.hhh........eeeehhhhhhh......eee.........eeeeeee.......eeeeee....eeeeee..........eeehhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------CYTC  PDB: A:52-131 UniProt: 81-160                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e2r A  36 DVAAPGAPEGVTALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYASPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGSTYEIKTVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLNNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 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:543
 aligned with NIRS_PARPN | P72181 from UniProtKB/Swiss-Prot  Length:596

    Alignment length:543
                                    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       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593   
           NIRS_PARPN    54 YEPSLDNLAQQDVAAPGAPEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 596
               SCOP domains d1e2rb1 B:25-135 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase                                d1e2rb2 B:136-567 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains -----------1e2rB01 B:36-135 Cytochrome c                                                                       1e2rB02 B:136-567  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh..............hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh......hhhhhh..hhhhhhhhhhhhhh........hhhhhhhhh....hhhhh........hhh..eeeee....eeeee......eeeeee....eeeeee.....eeeeee...eeeeee.......eeeeee......eeee.........eeeee.....eeeeee.....eeeeee...................eee.....eeeeee....eeeeee........eeeee.......eee.....eeeeee....eeeeee....eeeeeee...........eeeee...eeeeeee.....eeeeee.....hhhh...eeeeee................eeee......hhhhhh.eeeee.hhh........eeeehhhhhhh......eee.........eeeeeee.......eeeeee....eeeeee..........eeehhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------CYTC  PDB: B:52-131 UniProt: 81-160                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e2r B  25 YEPSLDNLAQQDVAAPGAPEGVTALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYASPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGSTYEIKTVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLNNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 567
                                    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       544       554       564
   Legend:   → Mismatch (orange background)
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  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 1E2R)

(-) 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 1gq1 1h9x 1h9y 1hcm 1hj3 1hj4 1hj5 1qks

(-) Related Entries Specified in the PDB File

1aof CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED FORM
1aom SUBSTRATE AND PRODUCT BOUND TO CYTOCHROME CD1 NITRITE REDUCTASE
1aoq CYTOCHROME CD1 NITRITE REDUCTASE WITH SUBSTRATE AND PRODUCT BOUND
1qks CYTOCHROME CD1 NITRITE REDUCTASE, OXIDISED FORM