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(-) Description

Title :  CYTOCHROME CD1 NITRITE REDUCTASE, CO COMPLEX
 
Authors :  T. Sjogren, M. Svensson-Ek, J. Hajdu, P. Brzezinski
Date :  28 Jan 00  (Deposition) - 24 Sep 00  (Release) - 13 Jul 11  (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, M. Svensson-Ek, J. Hajdu, P. Brzezinski
Proton-Coupled Structural Changes Upon Binding Of Carbon Monoxide To Cytochrome Cd(1): A Combined Flash Photolysis And X-Ray Crystallography Study
Biochemistry V. 39 10967 2000
PubMed-ID: 10998233  |  Reference-DOI: 10.1021/BI000179Q
(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
    Gene: NIRS
    Organism Scientific: PARACOCCUS PANTOTROPHUS
    Organism Taxid: 82367
    Other Details: ORGANISM FORMERLY KNOWN AS THIOSPHAERA PANTOTROPHA
    Synonym: CYTOCHROME CD1, CYTOCHROME OXIDASE, HYDROXYLAMINE REDUCTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric/Biological Unit (5, 11)
No.NameCountTypeFull Name
1CMO2Ligand/IonCARBON MONOXIDE
2DHE2Ligand/IonHEME D
3GOL3Ligand/IonGLYCEROL
4HEC1Ligand/IonHEME C
5SO43Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG 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:301 , ALA A:302 , ILE A:303 , HIS A:345 , ARG A:391 , PHE A:444 , GLN A:507 , TRP A:522 , GLY A:555 , PHE A:557 , CMO A:603 , HOH A:2083 , HOH A:2110 , HOH A:2389 , HOH A:2401 , HOH A:2402 , HOH A:2403 , HOH A:2404BINDING SITE FOR RESIDUE DHE A 602
02AC2SOFTWAREHIS A:388 , PHE A:444 , DHE A:602 , HOH A:2252BINDING SITE FOR RESIDUE CMO A 603
03AC3SOFTWAREPHE A:395 , VAL A:396 , PRO A:449 , SER A:451 , ILE A:475 , HOH A:2304 , HOH A:2405BINDING SITE FOR RESIDUE GOL A 611
04AC4SOFTWARETYR A:308 , ARG A:354 , LYS A:372BINDING SITE FOR RESIDUE SO4 A 621
05AC5SOFTWAREARG B:64 , CYS B:65 , CYS B:68 , HIS B:69 , THR B:77 , GLY B:78 , LYS B:79 , LEU B:89 , TYR B:93 , LEU B:94 , PHE B:97 , ILE B:98 , SER B:102 , ALA B:104 , GLY B:105 , MET B:106 , TRP B:109 , HOH B:2433BINDING SITE FOR RESIDUE HEC B 601
06AC6SOFTWAREARG 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 , GLY B:555 , PHE B:557 , CMO B:603 , HOH B:2121 , HOH B:2434 , HOH B:2435 , HOH B:2436 , HOH B:2437 , HOH B:2438 , HOH B:2439 , HOH B:2440BINDING SITE FOR RESIDUE DHE B 602
07AC7SOFTWAREHIS B:388 , DHE B:602 , HOH B:2287BINDING SITE FOR RESIDUE CMO B 603
08AC8SOFTWARELYS B:488 , THR B:489 , LEU B:490 , PRO B:491 , TRP B:495 , LEU B:539 , HOH B:2441BINDING SITE FOR RESIDUE GOL B 611
09AC9SOFTWAREARG B:174 , TYR B:197 , ARG B:216 , HOH B:2097BINDING SITE FOR RESIDUE GOL B 612
10BC1SOFTWARETYR B:308 , ARG B:354 , LYS B:372 , HOH B:2315 , HOH B:2442BINDING SITE FOR RESIDUE SO4 B 621
11BC2SOFTWAREGLY B:439 , GLY B:440 , ASN B:461 , GLU B:463 , HOH B:2336BINDING SITE FOR RESIDUE SO4 B 622

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DY7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DY7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DY7)

(-) PROSITE Motifs  (1, 1)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DY7)

(-) 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:434
 aligned with NIRS_PARPN | P72181 from UniProtKB/Swiss-Prot  Length:596

    Alignment length:434
                                   172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592    
           NIRS_PARPN   163 PPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 596
               SCOP domains d1dy7a_ A: C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1dy7A00 A:134-567  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhee..hhhhh........hhh.eeeeee....eeeeee.....eeeeee....eeeeee.....eeeeee...eeeeee.......eeeeee...eeeeeee.........eeeeeeee..eeeeee.....eeeeee..ee......ee....eeeeee.....eeeeee....eeeeee.....eeeeeeee....eeeeee.....eeeeee....eeeeee....eeeeeee...........eeeee...eeeeeee.....eeeeee............eeeeee........ee......eeee......hhhhhh.eeeee.hhh........eeeehhhhhhh......eeeeeee.....eeeeeee.......eeeeee....eeeeee.......eeeeeehhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dy7 A 134 PPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 567
                                   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    


Chain B from PDB  Type:PROTEIN  Length:536
 aligned with NIRS_PARPN | P72181 from UniProtKB/Swiss-Prot  Length:596

    Alignment length:536
                                    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       570       580       590      
           NIRS_PARPN    61 LAQQDVAAPGAPEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 596
               SCOP domains d1dy7b1 B:32-135 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase                         d1dy7b2 B:136-567 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----1dy7B01 B:36-135 Cytochrome c                                                                       1dy7B02 B:136-567  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhh........hhhhhhhhhee..hhhhh........hhh.eeeeee....eeeeee.....eeeeee....eeeeee.....eeeeee...eeeeee.......eeeeee...eeeeeee.........eeeeeeee..eeeeee.....eeeeee..ee......ee....eeeeee.....eeeeee....eeeeee.....eeeeeeee....eeeeee.....eeeeee....eeeeee....eeeeeee...........eeeee...eeeeeee.....eeeeee.....hhhh...eeeeee........ee......eeee......hhhhhh.eeeee.hhh.........eeehhhhhh.......eeeeeee.....eeeeeee.......eeeeee....eeeeee.......eeeeeehhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------CYTC  PDB: B:52-131 UniProt: 81-160                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dy7 B  32 LAQQDVAAPGAPEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 567
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561
   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, 3)

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

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DY7)

(-) 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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  1dy7
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  NIRS_PARPN | P72181
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  1.7.2.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        NIRS_PARPN | P72181: 1aof 1aom 1aoq 1e2r 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
1e2r CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED AND CYANIDE BOUND
1qks CYTOCHROME CD1 NITRITE REDUCTASE, OXIDISED FORM