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(-) Description

Title :  H294M MUTANT OF COPPER-CONTAINING NITRITE REDUCTASE FROM GEOBACILLUS THERMODENITRIFICANS
 
Authors :  Y. Fukuda, T. Inoue
Date :  16 Nov 14  (Deposition) - 18 Nov 15  (Release) - 18 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Beta Barrel, Nitrite Reduction, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Fukuda, T. Inoue
Structural Evidence Of The Flexibility Of The Cum Site
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NITRITE REDUCTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NIRK
    Mutation: YES
    Organism Scientific: GEOBACILLUS THERMODENITRIFICANS NG80-2
    Organism Taxid: 420246

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1ACY4Ligand/IonACETIC ACID
2CU7Ligand/IonCOPPER (II) ION
3MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 18)
No.NameCountTypeFull Name
1ACY12Ligand/IonACETIC ACID
2CU-1Ligand/IonCOPPER (II) ION
3MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:95 , CYS A:135 , HIS A:143 , MET A:148BINDING SITE FOR RESIDUE CU A 401
02AC2SOFTWAREHIS A:100 , HIS A:134 , MET A:294 , HOH A:861BINDING SITE FOR RESIDUE CU A 402
03AC3SOFTWAREHIS A:39 , HOH A:838BINDING SITE FOR RESIDUE CU A 403
04AC4SOFTWAREHIS A:42 , GLU A:53 , HIS A:83 , HOH A:559 , HOH A:620BINDING SITE FOR RESIDUE CU A 404
05AC5SOFTWAREPRO A:191 , GLU A:239 , HIS A:298 , HOH A:530 , HOH A:845 , HOH A:849BINDING SITE FOR RESIDUE CU A 405
06AC6SOFTWAREASP A:167 , ACY A:412 , HOH A:502 , HOH A:730 , HOH A:830 , HOH A:856BINDING SITE FOR RESIDUE CU A 406
07AC7SOFTWAREMET A:270 , HOH A:863BINDING SITE FOR RESIDUE CU A 407
08AC8SOFTWAREASP A:98 , HIS A:134 , VAL A:246 , HOH A:733 , HOH A:861BINDING SITE FOR RESIDUE ACY A 408
09AC9SOFTWAREHOH A:507 , HOH A:741BINDING SITE FOR RESIDUE ACY A 409
10BC1SOFTWAREASP A:163 , VAL A:166 , ASP A:167 , ARG A:168 , GLU A:169 , ARG A:229 , HOH A:669 , HOH A:829BINDING SITE FOR RESIDUE MPD A 410
11BC2SOFTWAREASP A:55 , SER A:192 , GLN A:300 , HOH A:595BINDING SITE FOR RESIDUE MPD A 411
12BC3SOFTWAREASP A:167 , VAL A:224 , GLY A:225 , CU A:406 , HOH A:501 , HOH A:830BINDING SITE FOR RESIDUE ACY A 412
13BC4SOFTWAREPRO A:128 , ASN A:258 , ASN A:260 , HOH A:567 , HOH A:661 , HOH A:705 , HOH A:707 , HOH A:752BINDING SITE FOR RESIDUE ACY A 413

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3X1F)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ala A:69 -Pro A:70
2Lys A:138 -Pro A:139
3Gly A:236 -Pro A:237

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3X1F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3X1F)

(-) Exons   (0, 0)

(no "Exon" information available for 3X1F)

(-) 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:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.........eeeeee..eeeeeeeeeeeeeeee..eeeeeeee........eeee..eeeeeeeee.........ee.....hhhhhh.......eeeeeeee...eeeeee....hhhhhhhh..eeeeeee......hhhhh.eeeeeeeeee....hhhhhhhh...eeeeeee.............hhhhhh.eeee...eeeeeeeeee....eeeee....eeeeee......eeeee..eee....eeeeeee....eeeeeee.hhhhhhh..eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3x1f A  18 IAAHKGVNQAPVPLKMERVGPHDVHIEMTAQITDIEIDKGKIYKAWTFNGQAPGPLVVVNEGDTIHFTLKNMDPVVPHSMDFHAVHASPSKDFIDVMPNKSGTFTYPANKPGVFMYHCGTKPVLQHIANGMHGVIIVKPKNGYPTDKEVDREYVLIQNEWYKYNDMNDFQNGVPSYVVFSSKALKPGDPNTNGDTFTLKEKPLLAKVGEKIRLYINNVGPNEVSSFHVVGTVFDDVYLDGNPNNHLQGMQTVMLPASGGAVVEFTVTRPGTYPIVTMQFNHAQKGAVAMLKVTETG 313
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 3X1F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3X1F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3X1F)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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UniProtKB/TrEMBL
        A4IL26_GEOTN | A4IL26: 3wkp 3wkq 3wni 3wnj 3x1e 3x1g 3x1n 4ysa 4ysd 4yso 4ysp 4ysq 4ysr 4yss 4yst 4ysu 4zk8

(-) Related Entries Specified in the PDB File

3x1e 3x1g