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(-) Description

Title :  ASSIMILATORY NITRITE REDUCTASE (NII3) - N226K MUTANT - LIGAND FREE FORM FROM TOBACCO LEAF
 
Authors :  S. Nakano, M. Takahashi, A. Sakamoto, H. Morikawa, K. Katayanagi
Date :  05 Dec 11  (Deposition) - 26 Sep 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Nii3 N226K Mutant, Ligand Free, 3 Alpha/Beta Domains, Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Nakano, M. Takahashi, A. Sakamoto, H. Morikawa, K. Katayanagi
X-Ray Crystal Structure Of A Mutant Assimilatory Nitrite Reductase That Shows Sulfite Reductase-Like Activity
Chem. Biodivers. V. 9 1989 2012
PubMed-ID: 22976986  |  Reference-DOI: 10.1002/CBDV.201100442

(-) Compounds

Molecule 1 - NITRITE REDUCTASE
    Chains: A
    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: UNP RESIDUES 19-580
    Gene: NII3
    Mutation: YES
    Organism Common: TOBACCO
    Organism Scientific: NICOTIANA TABACUM
    Organism Taxid: 4097

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2K1Ligand/IonPOTASSIUM ION
3SF41Ligand/IonIRON/SULFUR CLUSTER
4SRM1Ligand/IonSIROHEME

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:96 , ARG A:98 , 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 , LYS A:226 , PHE A:264 , PHE A:265 , SER A:266 , ARG A:309 , GLN A:402 , CYS A:440 , THR A:441 , CYS A:446 , GLN A:448 , ASN A:483 , THR A:484 , CYS A:485 , GLN A:487 , SF4 A:602 , CL A:606 , HOH A:1004 , HOH A:1005 , HOH A:1022 , HOH A:1031 , HOH A:1039 , HOH A:1054 , HOH A:1060 , HOH A:1065 , HOH A:1087 , HOH A:1133 , HOH A:1166 , HOH A:1188 , HOH A:1221 , HOH A:1285 , HOH A:1429 , HOH A:1471 , HOH A:1894BINDING SITE FOR RESIDUE SRM A 601
2AC2SOFTWARECYS A:440 , CYS A:446 , ALA A:449 , THR A:479 , GLY A:480 , CYS A:481 , ASN A:483 , THR A:484 , CYS A:485 , SRM A:601BINDING SITE FOR RESIDUE SF4 A 602
3AC3SOFTWAREILE A:371 , GLU A:401 , GLN A:402 , ASN A:403 , HOH A:1013 , HOH A:1027BINDING SITE FOR RESIDUE K A 603
4AC4SOFTWAREMET A:175 , HOH A:1002 , HOH A:1285BINDING SITE FOR RESIDUE CL A 604
5AC5SOFTWAREARG A:99 , LYS A:100 , HOH A:1133BINDING SITE FOR RESIDUE CL A 605
6AC6SOFTWAREARG A:109 , ARG A:179 , LYS A:224 , SRM A:601BINDING SITE FOR RESIDUE CL A 606

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VLX)

(-) 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:538
 aligned with Q76KB0_TOBAC | Q76KB0 from UniProtKB/TrEMBL  Length:587

    Alignment length:538
                                    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        
         Q76KB0_TOBAC    43 VAAERLEPRVEEKDGYWILKEQFRKGINPQEKVKIEKEPMKLFMENGIEELAKIPIEEIDQSKLTKDDIDVRLKWLGLFHRRKNQYGRFMMRLKLPNGVTTSAQTRYLASVIRKYGKEGCADITTRQNWQIRGVVLPDVPEILKGLAEVGLTSLQSGMDNVRNPVGNPLAGIDPEEIVDTRPYTNLLSQFITGNSRGNPAVSNLPRKWNPCVVGSHDLYEHPHINDLAYMPATKDGRFGFNLLVGGFFSAKRCDEAIPLDAWVPADDVVPVCKAILEAFRDLGFRGNRQKCRMMWLIDELGVEGFRAEVEKRMPQQQLERASPEDLVQKQWERRDYLGVHPQKQEGYSFIGLHIPVGRVQADDMDELARLADEYGSGEIRLTVEQNIIIPNIETSKIEALLKEPVLSTFSPDPPILMKGLVACTGNQFCGQAIIETKARSLKITEEVQRQVSLTKPVRMHWTGCPNTCAQVQVADIGFMGCLTRDKNGKTVEGADVFLGGRIGSDSHLGEVYKKAVPCDDLVPLVVDLLVNNFGAVPR 580
               SCOP domains d3vlxa1 A:18-174 automated matches                                                                                                                           d3vlxa2 A:175-345 automated matches                                                                                                                                        d3vlxa3 A:346-429 automated matches                                                 d3vlxa4 A:430-555 automated matches                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeee..eeee.hhhh...hhhhhhhhhh..hhhhhh.hhhhhh..hhhhhh.hhhhhhhhhhhhhhh.eee.......eeeee..hhh.eeehhhhhhhhhhhhhhhhhheeee.....eeeeeee..hhhhhhhhhhhh..............................hhhhhhhhhhhhhh....hhhhh.......eee........hhhhh.eeeeeeee..eeeeeeee............eeeeeeee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................eeee.....eeeeee.hhh.eehhhhhhhhhhhhhhhh..eeee.....eeeeeee..hhhhhhhhhhhhh.....hhhhhh.ee.hhhhh.......hhhhhhhhhhhhhhhee......eeee.......hhhhh.eeeeeeeee.....eeeeeeeee...........eeeeeeee..hhhhhhhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vlx A  18 VAAERLEPRVEEKDGYWILKEQFRKGINPQEKVKIEKEPMKLFMENGIEELAKIPIEEIDQSKLTKDDIDVRLKWLGLFHRRKNQYGRFMMRLKLPNGVTTSAQTRYLASVIRKYGKEGCADITTRQNWQIRGVVLPDVPEILKGLAEVGLTSLQSGMDNVRNPVGNPLAGIDPEEIVDTRPYTNLLSQFITGNSRGNPAVSNLPRKWKPCVVGSHDLYEHPHINDLAYMPATKDGRFGFNLLVGGFFSAKRCDEAIPLDAWVPADDVVPVCRAILEAFRDLGFRGNRQKCRMMWLIDELGVEGFRAEVEKRMPQQQLERASPEDLVQKQWERRDYLGVHPQKQEGYSFIGLHIPVGRVQADDMDELARLADEYGSGEIRLTVEQNIIIPNIETSKIEALLKEPVLSTFSPDPPILMKGLVACTGNQFCGQAIIETKARSLKITEEVQRQVSLTKPVRMHWTGCPNTCAQVQVADIGFMGCLTRDKNGKTVEGADVFLGGRIGSDSHLGEVYKKAVPCDDLVPLVVDLLVNNFGAVPR 555
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (2, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q76KB0_TOBAC | Q76KB0)
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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  1.7.7.1
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 Related Entries

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

UniProtKB/TrEMBL
        Q76KB0_TOBAC | Q76KB0: 3b0g 3b0j 3b0l 3b0m 3b0n 3vkp 3vkq 3vkr 3vks 3vkt 3vly 3vlz 3vm0 3vm1

(-) Related Entries Specified in the PDB File

3b0g ASSIMILATORY NITRITE REDUCTASE (NII3) FROM TOBBACO LEAF
3vly
3vlz
3vm0
3vm1