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(-) Description

Title :  ESHERICHIA COLI NITRITE REDUCTASE NRFA H264N
 
Authors :  T. A. Clarke, M. J. Edwards, C. W. J. Lockwood
Date :  01 Oct 14  (Deposition) - 11 Mar 15  (Release) - 18 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nitrite Reductase Cytochrome Mutagenesis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. W. Lockwood, B. Burlat, M. R. Cheesman, M. Kern, J. Simon, T. A. Clarke, D. J. Richardson, J. N. Butt
Resolution Of Key Roles For The Distal Pocket Histidine In Cytochrome C Nitrite Reductases.
J. Am. Chem. Soc. V. 137 3059 2015
PubMed-ID: 25658043  |  Reference-DOI: 10.1021/JA512941J

(-) Compounds

Molecule 1 - CYTOCHROME C-552
    Chains: A, B
    EC Number: 1.7.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: JCB4083A
    Expression System Taxid: 562
    Gene: NRFA, B4070, JW4031
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Synonym: AMMONIA-FORMING CYTOCHROME C NITRITE REDUCTASE,CYTOCHROME C NITRITE REDUCTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3HEM10Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:89 , ASP A:100 , THR A:104 , ARG A:106 , CYS A:122 , CYS A:125 , LYS A:126 , CYS A:212 , HIS A:213 , TYR A:216 , VAL A:225 , ASN A:264 , HIS A:388 , HEM A:503 , HOH A:638 , HOH A:657 , HOH A:658 , HOH A:660 , HOH A:692 , HOH A:705 , HOH A:753 , HOH A:771 , HOH A:999binding site for residue HEM A 501
02AC2SOFTWAREHIS A:49 , GLN A:52 , TYR A:53 , TRP A:56 , GLY A:159 , CYS A:160 , CYS A:163 , HIS A:164 , PHE A:171 , GLY A:174 , PRO A:176 , ARG A:201 , GLN A:205 , ILE A:283 , MET A:287 , LYS A:289 , TYR A:298 , THR A:299 , HIS A:301 , HEM A:503 , HOH A:773 , HOH A:883binding site for residue HEM A 502
03AC3SOFTWAREGLN A:62 , PRO A:91 , ARG A:92 , GLY A:93 , HIS A:94 , PHE A:96 , ALA A:97 , ASP A:100 , CYS A:125 , LEU A:158 , VAL A:208 , CYS A:209 , CYS A:212 , HIS A:213 , HIS A:286 , MET A:287 , ILE A:303 , HEM A:501 , HEM A:502 , HEM A:504 , CA A:507 , HOH A:662 , HOH A:667 , HOH A:882binding site for residue HEM A 503
04AC4SOFTWAREHIS A:213 , TRP A:270 , HIS A:275 , VAL A:280 , THR A:281 , CYS A:282 , CYS A:285 , HIS A:286 , ASN A:305 , PRO A:306 , VAL A:329 , HIS A:388 , HIS A:391 , MET A:392 , HIS A:393 , HEM A:503 , HEM A:505 , CA A:507 , HOH A:697 , HOH A:752 , HOH A:767 , HOH A:798 , HOH A:824binding site for residue HEM A 504
05AC5SOFTWAREHIS A:275 , VAL A:280 , PHE A:307 , THR A:313 , CYS A:314 , CYS A:317 , HIS A:318 , ARG A:332 , MET A:392 , HEM A:504 , EDO A:508 , HOH A:706 , HOH A:928 , HIS B:318 , GLN B:320 , HEM B:505binding site for residue HEM A 505
06AC6SOFTWAREGLU A:215 , TYR A:216 , LYS A:261 , GLN A:263 , HOH A:644 , HOH A:653binding site for residue CA A 506
07AC7SOFTWAREPRO A:91 , HEM A:503 , HEM A:504 , HOH A:662 , HOH A:688 , HOH A:697 , HOH A:798binding site for residue CA A 507
08AC8SOFTWARECYS A:317 , HEM A:505 , HEM B:505binding site for residue EDO A 508
09AC9SOFTWAREASP A:308 , PHE A:310 , ALA A:311 , LYS A:322binding site for residue EDO A 509
10AD1SOFTWARETYR B:88 , ASN B:89 , ASP B:100 , THR B:104 , ARG B:106 , LEU B:118 , CYS B:122 , CYS B:125 , LYS B:126 , CYS B:212 , HIS B:213 , TYR B:216 , ASN B:264 , HIS B:388 , HEM B:503 , HOH B:633 , HOH B:645 , HOH B:674 , HOH B:690 , HOH B:699 , HOH B:781 , HOH B:898binding site for residue HEM B 501
11AD2SOFTWAREHIS B:49 , GLN B:52 , TYR B:53 , TRP B:56 , GLY B:159 , CYS B:160 , CYS B:163 , HIS B:164 , PHE B:171 , GLY B:174 , LEU B:178 , ARG B:201 , GLN B:205 , MET B:287 , LYS B:289 , TYR B:298 , THR B:299 , HIS B:301 , HEM B:503 , HOH B:676 , HOH B:748 , HOH B:910binding site for residue HEM B 502
12AD3SOFTWAREGLU B:215 , TYR B:216 , LYS B:261 , GLN B:263 , HOH B:638 , HOH B:646binding site for residue CA B 506
13AD4SOFTWAREPRO B:91 , HEM B:503 , HEM B:504 , HOH B:653 , HOH B:701 , HOH B:901binding site for residue CA B 507
14AD5SOFTWAREARG B:74 , ASP B:345 , HIS B:349 , ILE B:431 , ILE B:434 , HOH B:786 , HOH B:872binding site for residue EDO B 508
15AD6SOFTWAREGLN B:62 , PRO B:91 , ARG B:92 , GLY B:93 , HIS B:94 , PHE B:96 , ALA B:97 , ASP B:100 , CYS B:125 , LYS B:126 , LEU B:158 , SER B:206 , MET B:207 , VAL B:208 , GLY B:210 , GLN B:211 , CYS B:212 , HIS B:213 , CYS B:282 , HIS B:286 , ILE B:303 , HEM B:501 , HEM B:502 , HEM B:504 , CA B:507 , HOH B:653 , HOH B:669 , HOH B:878binding site for Di-peptide HEM B 503 and CYS B 209
16AD7SOFTWARESER B:206 , CYS B:209 , HIS B:213 , TRP B:270 , HIS B:275 , THR B:281 , ILE B:283 , ASP B:284 , CYS B:285 , HIS B:286 , HIS B:388 , HIS B:391 , MET B:392 , HIS B:393 , HEM B:503 , HEM B:505 , CA B:507 , HOH B:813 , HOH B:901binding site for Di-peptide HEM B 504 and CYS B 282
17AD8SOFTWAREHIS A:318 , GLN A:320 , HEM A:505 , EDO A:508 , ILE B:274 , HIS B:275 , ASN B:278 , VAL B:280 , PHE B:307 , PHE B:310 , THR B:313 , ALA B:315 , ASN B:316 , CYS B:317 , HIS B:318 , ARG B:332 , MET B:392 , HEM B:504 , HOH B:803 , HOH B:830binding site for Di-peptide HEM B 505 and CYS B 314

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WJY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WJY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WJY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WJY)

(-) Exons   (0, 0)

(no "Exon" information available for 4WJY)

(-) 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:441
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh..........hhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhh.......hhhhhh...hhhhhh........hhhhhhhhhhh..hhhhhhhhhhhhhhhh......eee....eee.......hhhhhhhhhhhh....ee......ee.....hhhhhhhhhhhhhh..hhhhhhh.eee.....eee.....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wjy A  37 TVEAKNETFAPQHPDQYLSWKATSEQSERVDALAEDPRLVILWAGYPFSRDYNKPRGHAFAVTDVRETLRTGAPKNAEDGPLPMACWSCKSPDVARLIQKDGEDGYFHGKWARGGPEIVNNLGCADCHNTASPEFAKGKPELTLSRPYAARAMEAIGKPFEKAGRFDQQSMVCGQCHVEYYFDGKNKAVKFPWDDGMKVENMEQYYDKIAFSDWTNSLSKTPMLKAQNPEYETWTAGIHGKNNVTCIDCHMPKVQNAEGKLYTDHKIGNPFDNFAQTCANCHTQDKAALQKVVAERKQSINDLKIKVEDQLVHAHFEAKAALDAGATEAEMKPIQDDIRHAQWRWDLAIASHGIHMHAPEEGLRMLGTAMDKAADARTKLARLLATKGITHEIQIPDISTKEKAQQAIGLNMEQIKAEKQDFIKTVIPQWEEQARKNGLLS 477
                                    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 


Chain B from PDB  Type:PROTEIN  Length:441
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh..........hhhhhh...hhhhhhhhhhhhhhhhh.hhhhhh.......hhhhhh...hhhhhh........hhhhhhhhhhh.......hhhhhhhhhhh......eee....eee.......hhhhhhhhhhhh....ee......ee.....hhhhhhhhhhhhhh..hhhhhhh.eee.....eee.....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wjy B  37 TVEAKNETFAPQHPDQYLSWKATSEQSERVDALAEDPRLVILWAGYPFSRDYNKPRGHAFAVTDVRETLRTGAPKNAEDGPLPMACWSCKSPDVARLIQKDGEDGYFHGKWARGGPEIVNNLGCADCHNTASPEFAKGKPELTLSRPYAARAMEAIGKPFEKAGRFDQQSMVCGQCHVEYYFDGKNKAVKFPWDDGMKVENMEQYYDKIAFSDWTNSLSKTPMLKAQNPEYETWTAGIHGKNNVTCIDCHMPKVQNAEGKLYTDHKIGNPFDNFAQTCANCHTQDKAALQKVVAERKQSINDLKIKVEDQLVHAHFEAKAALDAGATEAEMKPIQDDIRHAQWRWDLAIASHGIHMHAPEEGLRMLGTAMDKAADARTKLARLLATKGITHEIQIPDISTKEKAQQAIGLNMEQIKAEKQDFIKTVIPQWEEQARKNGLLS 477
                                    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
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (0, 0)

(no "SCOP Domain" information available for 4WJY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WJY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WJY)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        NRFA_ECOLI | P0ABK9: 1gu6 2rdz 2rf7 3l1t 3tor

(-) Related Entries Specified in the PDB File

2rdz 2RDZ IS THE WILD TYPE PROTEIN.
2rf7 2RF7 HAS A MODIFIED ACTIVE SITE