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(-) Description

Title :  ASSIMILATORY NITRITE REDUCTASE (NII4) FROM TOBBACO ROOT
 
Authors :  S. Nakano, M. Takahashi, A. Sakamoto, H. Morikawa, K. Katayanagi
Date :  09 Jun 11  (Deposition) - 22 Feb 12  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Siroheme, Fe4S4 Binding Protein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Nakano, M. Takahashi, A. Sakamoto, H. Morikawa, K. Katayanagi
Structure-Function Relationship Of Assimilatory Nitrite Reductases From The Leaf And Root Of Tobacco Based On High Resolution Structures
Protein Sci. V. 21 383 2012
PubMed-ID: 22238192  |  Reference-DOI: 10.1002/PRO.2025

(-) Compounds

Molecule 1 - NITRITE REDUCTASE
    Chains: A, B
    EC Number: 1.7.7.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES IN UNP 19-584
    Gene: NII4
    Organism Common: TOBACCO
    Organism Scientific: NICOTIANA TABACUM
    Organism Taxid: 4097
    Synonym: NII4

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2K2Ligand/IonPOTASSIUM ION
3SF42Ligand/IonIRON/SULFUR CLUSTER
4SRM2Ligand/IonSIROHEME
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2K-1Ligand/IonPOTASSIUM ION
3SF41Ligand/IonIRON/SULFUR CLUSTER
4SRM1Ligand/IonSIROHEME
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2K-1Ligand/IonPOTASSIUM ION
3SF41Ligand/IonIRON/SULFUR CLUSTER
4SRM1Ligand/IonSIROHEME

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:96 , ARG A:98 , MET A:107 , ARG A:109 , THR A:141 , THR A:142 , ARG A:143 , ASN A:145 , GLN A:147 , ARG A:149 , ARG A:223 , LYS A:224 , ASN A:226 , PHE A:264 , PHE A:265 , SER A:266 , PRO A:267 , GLN A:306 , ARG A:309 , GLN A:402 , CYS A:441 , THR A:442 , LYS A:449 , ASN A:484 , SER A:485 , CYS A:486 , GLN A:488 , SF4 A:602 , HOH A:1001 , HOH A:1030 , HOH A:1069 , HOH A:1111 , HOH A:1114 , HOH A:1122 , HOH A:1130 , HOH A:1131 , HOH A:1136 , HOH A:1140 , HOH A:1146BINDING SITE FOR RESIDUE SRM A 601
02AC2SOFTWARECYS A:441 , CYS A:447 , ALA A:450 , THR A:480 , GLY A:481 , CYS A:482 , ASN A:484 , CYS A:486 , SRM A:601BINDING SITE FOR RESIDUE SF4 A 602
03AC3SOFTWAREILE A:371 , GLU A:401 , GLN A:402 , ASN A:403 , HOH A:1051BINDING SITE FOR RESIDUE K A 603
04AC4SOFTWAREMET A:175 , ARG A:179 , HOH A:1130BINDING SITE FOR RESIDUE CL A 604
05AC5SOFTWAREARG A:99 , LYS A:100 , GLY A:448BINDING SITE FOR RESIDUE CL A 605
06AC6SOFTWAREPHE B:96 , ARG B:98 , MET B:107 , ARG B:109 , THR B:141 , THR B:142 , ARG B:143 , ASN B:145 , GLN B:147 , ARG B:149 , ARG B:223 , LYS B:224 , ASN B:226 , PHE B:264 , PHE B:265 , SER B:266 , PRO B:267 , GLN B:306 , ARG B:309 , GLN B:402 , CYS B:441 , THR B:442 , LYS B:449 , ASN B:484 , SER B:485 , CYS B:486 , GLN B:488 , SF4 B:602 , HOH B:705 , HOH B:712 , HOH B:758 , HOH B:768 , HOH B:769 , HOH B:804 , HOH B:809 , HOH B:814 , HOH B:823 , HOH B:877 , HOH B:942BINDING SITE FOR RESIDUE SRM B 601
07AC7SOFTWARECYS B:441 , CYS B:447 , ALA B:450 , THR B:480 , GLY B:481 , CYS B:482 , ASN B:484 , CYS B:486 , SRM B:601BINDING SITE FOR RESIDUE SF4 B 602
08AC8SOFTWAREILE B:371 , GLU B:401 , GLN B:402 , ASN B:403 , HOH B:786BINDING SITE FOR RESIDUE K B 603
09AC9SOFTWAREMET B:175 , HOH B:804BINDING SITE FOR RESIDUE CL B 604
10BC1SOFTWAREARG B:99 , LYS B:100 , GLY B:448 , HOH B:832 , HOH B:893 , HOH B:942BINDING SITE FOR RESIDUE CL B 605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B0H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3B0H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B0H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B0H)

(-) Exons   (0, 0)

(no "Exon" information available for 3B0H)

(-) Sequences/Alignments

Asymmetric 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:536
 aligned with Q76KA9_TOBAC | Q76KA9 from UniProtKB/TrEMBL  Length:584

    Alignment length:536
                                    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       571      
         Q76KA9_TOBAC    42 SERLEPRVEEKDGYWVLKEKFRQGINPAEKAKIEKEPMKLFMENGIEDLAKISLEEIEGSKLTKDDIDVRLKWLGLFHRRKHHYGRFMMRLKLPNGVTTSSQTRYLASVIRKYGKDGCADVTTRQNWQIRGVVLPDVPEILKGLDEVGLTSLQSGMDNVRNPVGNPLAGIDPHEIVDTRPYTNLLSQYVTANFRGNPAVTNLPRKWNVCVIGSHDLYEHPQINDLAYMPATKDGRFGFNLLVGGFFSPKRCAEAVPLDAWVPADDVVPVCKAILEAYRDLGTRGNRQKTRMMWLVDELGVEGFRAEVVKRMPQQKLDRESTEDLVQKQWERREYLGVHPQKQEGYSFVGLHIPVGRVQADDMDELARLADEYGSGELRLTVEQNIIIPNVKNSKIEALLNEPLLKNRFSTDPPILMKNLVACTGNQFCGKAIIETKARSMKITEEVQLLVSITQPVRMHWTGCPNSCAQVQVADIGFMGCLTRKEGKTVEGADVYLGGRIGSDSHLGDVYKKSVPCEDLVPIIVDLLVDNFGAVPR 577
               SCOP domains d3b0ha1 A:20-174 automated matches                                                                                                                         d3b0ha2 A:175-345 automated matches                                                                                                                                        d3b0ha3 A:346-430 automated matches                                                  d3b0ha4 A:431-555 automated matches                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee..eeee.hhhh...hhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.eee........eeee..hhh.eeehhhhhhhhhhhhhhhhhheeee.....eeeeeehhhhhhhhhhhhhhh..............................hhhhhhhhhhhhhh....hhhhh.......eee........hhhhh.eeeeeeee..eeeeeeee..ee....ee..eeeeeeee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..........................eeee.....eeeeee.hhh.eehhhhhhhhhhhhhhhh..eeee.....eeeeeee..hhhhhhhhhhhhhh.....hhhhhheee.............hhhhhhhhhhhhhhhh.......eeee.......hhhhh.eeeeeeeee....eeeeeeeee...........eeeeeeee..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b0h A  20 SERLEPRVEEKDGYWVLKEKFRQGINPAEKAKIEKEPMKLFMENGIEDLAKISLEEIEGSKLTKDDIDVRLKWLGLFHRRKHHYGRFMMRLKLPNGVTTSSQTRYLASVIRKYGKDGCADVTTRQNWQIRGVVLPDVPEILKGLDEVGLTSLQSGMDNVRNPVGNPLAGIDPHEIVDTRPYTNLLSQYVTANFRGNPAVTNLPRKWNVCVIGSHDLYEHPQINDLAYMPATKDGRFGFNLLVGGFFSPKRCAEAVPLDAWVPADDVVPVCKAILEAYRDLGTRGNRQKTRMMWLVDELGVEGFRAEVVKRMPQQKLDRESTEDLVQKQWERREYLGVHPQKQEGYSFVGLHIPVGRVQADDMDELARLADEYGSGELRLTVEQNIIIPNVKNSKIEALLNEPLLKNRFSTDPPILMKNLVACTGNQFCGKAIIETKARSMKITEEVQLLVSITQPVRMHWTGCPNSCAQVQVADIGFMGCLTRKEGKTVEGADVYLGGRIGSDSHLGDVYKKSVPCEDLVPIIVDLLVDNFGAVPR 555
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549      


Chain B from PDB  Type:PROTEIN  Length:535
 aligned with Q76KA9_TOBAC | Q76KA9 from UniProtKB/TrEMBL  Length:584

    Alignment length:535
                                    52        62        72        82        92       102       112       122       132       142       152       162       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     
         Q76KA9_TOBAC    43 ERLEPRVEEKDGYWVLKEKFRQGINPAEKAKIEKEPMKLFMENGIEDLAKISLEEIEGSKLTKDDIDVRLKWLGLFHRRKHHYGRFMMRLKLPNGVTTSSQTRYLASVIRKYGKDGCADVTTRQNWQIRGVVLPDVPEILKGLDEVGLTSLQSGMDNVRNPVGNPLAGIDPHEIVDTRPYTNLLSQYVTANFRGNPAVTNLPRKWNVCVIGSHDLYEHPQINDLAYMPATKDGRFGFNLLVGGFFSPKRCAEAVPLDAWVPADDVVPVCKAILEAYRDLGTRGNRQKTRMMWLVDELGVEGFRAEVVKRMPQQKLDRESTEDLVQKQWERREYLGVHPQKQEGYSFVGLHIPVGRVQADDMDELARLADEYGSGELRLTVEQNIIIPNVKNSKIEALLNEPLLKNRFSTDPPILMKNLVACTGNQFCGKAIIETKARSMKITEEVQLLVSITQPVRMHWTGCPNSCAQVQVADIGFMGCLTRKEGKTVEGADVYLGGRIGSDSHLGDVYKKSVPCEDLVPIIVDLLVDNFGAVPR 577
               SCOP domains d3b0hb1 B:21-174 automated matches                                                                                                                        d3b0hb2 B:175-345 automated matches                                                                                                                                        d3b0hb3 B:346-430 automated matches                                                  d3b0hb4 B:431-555 automated matches                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..eeee.hhhh...hhhhhhhhhh..hhhhhh.hhhhhh..hhhhhh.hhhhhhhhhhhhhhh.eee........eeee..hhh.eeehhhhhhhhhhhhhhhhhheeee.....eeeeeehhhhhhhhhhhhhhh..............................hhhhhhhhhhhhh.....hhhhh.......eee........hhhhh.eeeeeeee..eeeeeeee..ee....ee..eeeeeeee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee............eeee.....eeeeee.hhh.eehhhhhhhhhhhhhhhh..eeee.....eeeeeee..hhhhhhhhhhhhhh.....hhhhhheee.hhhhh.......hhhhhhhhhhhhhhhee......eeee.......hhhhh.eeeeeeeee....eeeeeeeee...........eeeeeeee..hhhhhhhhhhhhhh..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b0h B  21 ERLEPRVEEKDGYWVLKEKFRQGINPAEKAKIEKEPMKLFMENGIEDLAKISLEEIEGSKLTKDDIDVRLKWLGLFHRRKHHYGRFMMRLKLPNGVTTSSQTRYLASVIRKYGKDGCADVTTRQNWQIRGVVLPDVPEILKGLDEVGLTSLQSGMDNVRNPVGNPLAGIDPHEIVDTRPYTNLLSQYVTANFRGNPAVTNLPRKWNVCVIGSHDLYEHPQINDLAYMPATKDGRFGFNLLVGGFFSPKRCAEAVPLDAWVPADDVVPVCKAILEAYRDLGTRGNRQKTRMMWLVDELGVEGFRAEVVKRMPQQKLDRESTEDLVQKQWERREYLGVHPQKQEGYSFVGLHIPVGRVQADDMDELARLADEYGSGELRLTVEQNIIIPNVKNSKIEALLNEPLLKNRFSTDPPILMKNLVACTGNQFCGKAIIETKARSMKITEEVQLLVSITQPVRMHWTGCPNSCAQVQVADIGFMGCLTRKEGKTVEGADVYLGGRIGSDSHLGDVYKKSVPCEDLVPIIVDLLVDNFGAVPR 555
                                    30        40        50        60        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
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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, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3B0H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B0H)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q76KA9_TOBAC | Q76KA9)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0048307    ferredoxin-nitrite reductase activity    Catalysis of the reaction: NH3 + 2 H2O + 6 oxidized ferredoxin = nitrite + 6 reduced ferredoxin + 7 H+.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.

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3b0g 3b0j 3b0l 3b0m 3b0n