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(-) Description

Title :  M144Q STRUCTURE OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
 
Authors :  M. A. Hough, M. J. Ellis, S. Antonyuk, R. W. Strange, G. Sawers, R. R. Eady, S. S. Hasnain
Date :  18 Apr 05  (Deposition) - 26 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Keywords :  Oxidoreductase, Dentrification, Nitrite Reductase, M168Q, Mutant, Electron Transfer, Nitrate Assimilation, Periplasmic (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Hough, M. J. Ellis, S. Antonyuk, R. W. Strange, G. Sawers, R. R. Eady, S. S. Hasnain
High Resolution Structural Studies Of Mutants Provide Insights Into Catalysis And Electron Transfer Processes In Copper Nitrite Reductase
J. Mol. Biol. V. 350 300 2005
PubMed-ID: 15927201  |  Reference-DOI: 10.1016/J.JMB.2005.04.006

(-) Compounds

Molecule 1 - DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism ScientificACHROMOBACTER XYLOSOXIDANS
    Organism Taxid85698
    SynonymNITRITE REDUCTASE, NIR
 
Molecule 2 - DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism ScientificACHROMOBACTER XYLOSOXIDANS
    Organism Taxid85698
    SynonymNITRITE REDUCTASE, NIR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (3x)A 
Biological Unit 2 (3x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1CU4Ligand/IonCOPPER (II) ION
2SO44Ligand/IonSULFATE ION
3ZN10Ligand/IonZINC ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2SO46Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2SO46Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:89 , CYS A:130 , HIS A:139 , GLN A:144BINDING SITE FOR RESIDUE CU A1337
02AC2SOFTWAREHIS A:94 , HIS A:129 , HIS A:300 , HOH A:2177BINDING SITE FOR RESIDUE CU A1338
03AC3SOFTWAREHIS A:165 , ASP A:167 , HOH A:2417 , GLU B:195BINDING SITE FOR RESIDUE ZN A1339
04AC4SOFTWAREHIS A:70 , ASP A:73 , HOH A:2418 , HOH A:2419BINDING SITE FOR RESIDUE ZN A1340
05AC5SOFTWAREHIS A:313 , SO4 A:1344 , SO4 A:1345 , HOH A:2420BINDING SITE FOR RESIDUE ZN A1341
06AC6SOFTWAREHIS A:8 , GLU A:34 , HOH A:2421 , HOH A:2422BINDING SITE FOR RESIDUE ZN A1342
07AC7SOFTWAREASP A:4 , HIS A:8BINDING SITE FOR RESIDUE ZN A1343
08AC8SOFTWAREHIS A:313 , ZN A:1341 , SO4 A:1345 , HOH A:2424 , HOH A:2425BINDING SITE FOR RESIDUE SO4 A1344
09AC9SOFTWAREHIS A:313 , ZN A:1341 , SO4 A:1344 , HOH A:2426 , HOH A:2427 , HOH A:2428 , HOH A:2429BINDING SITE FOR RESIDUE SO4 A1345
10BC1SOFTWAREHIS B:89 , CYS B:130 , HIS B:139 , GLN B:144BINDING SITE FOR RESIDUE CU B1337
11BC2SOFTWAREHIS B:94 , HIS B:129 , HIS B:300 , HOH B:2136BINDING SITE FOR RESIDUE CU B1338
12BC3SOFTWAREHIS B:70 , ASP B:73 , HOH B:2351BINDING SITE FOR RESIDUE ZN B1339
13BC4SOFTWAREGLU A:195 , HIS B:165 , ASP B:167 , HOH B:2352BINDING SITE FOR RESIDUE ZN B1340
14BC5SOFTWAREHIS B:313 , SO4 B:1344 , SO4 B:1345 , HOH B:2353BINDING SITE FOR RESIDUE ZN B1341
15BC6SOFTWAREHIS B:8 , GLU B:34 , HOH B:2354 , HOH B:2355 , HOH B:2356BINDING SITE FOR RESIDUE ZN B1342
16BC7SOFTWAREASP B:4 , HIS B:8BINDING SITE FOR RESIDUE ZN B1343
17BC8SOFTWAREHIS B:313 , ZN B:1341 , SO4 B:1345 , HOH B:2358 , HOH B:2359 , HOH B:2361BINDING SITE FOR RESIDUE SO4 B1344
18BC9SOFTWAREHIS B:313 , ZN B:1341 , SO4 B:1344 , HOH B:2358 , HOH B:2362 , HOH B:2363BINDING SITE FOR RESIDUE SO4 B1345

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BP8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:16 -Pro A:17
2Met A:62 -Pro A:63
3Pro B:16 -Pro B:17
4Met B:62 -Pro B:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BP8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BP8)

(-) Exons   (0, 0)

(no "Exon" information available for 2BP8)

(-) 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:335
 aligned with O68601_ALCXX | O68601 from UniProtKB/TrEMBL  Length:360

    Alignment length:335
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355     
         O68601_ALCXX    26 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIPR 360
               SCOP domains d2bp8a1 A:2-159 automated matches                                                                                                                             d2bp8a2 A:160-336 automated matches                                                                                                                                               SCOP domains
               CATH domains 2bp8A01 A:2-152 Cupredoxins -  blue copper proteins                                                                                                    2bp8A02 A:153-319 Cupredoxins -  blue copper proteins                                                                                                                  ----------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee................eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eee....eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bp8 A   2 DADKLPHTKVTLVAPPQVHPHEQASKTGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGQSGTLMVLPRDGLKDPEGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIPR 336
                                    11        21        31        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     

Chain B from PDB  Type:PROTEIN  Length:335
 aligned with O68601_ALCXX | O68601 from UniProtKB/TrEMBL  Length:360

    Alignment length:335
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355     
         O68601_ALCXX    26 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIPR 360
               SCOP domains d2bp8b1 B:2-159 automated matches                                                                                                                             d2bp8b2 B:160-336 automated matches                                                                                                                                               SCOP domains
               CATH domains 2bp8B01 B:2-152 Cupredoxins -  blue copper proteins                                                                                                    2bp8B02 B:153-319 Cupredoxins -  blue copper proteins                                                                                                                  ----------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee................eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eee....eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bp8 B   2 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGQSGTLMVLPRDGLKDPEGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIPR 336
                                    11        21        31        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     

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BP8)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O68601_ALCXX | O68601)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    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:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
    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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 Related Entries

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

UniProtKB/TrEMBL
        O68601_ALCXX | O686011bq5 1gs6 1gs7 1gs8 1hau 1haw 1ndt 1oe1 1oe2 1oe3 1wa0 1wa1 1wa2 1wae 2bo0 2bp0 2jfc 2vm3 2vm4 2vmj 2vn3 2vw4 2vw6 2vw7 2xwz 2xx0 2xx1 2xxf 2xxg 2zon 4csp 4csz 5b1j 5b1k

(-) Related Entries Specified in the PDB File

1bq5 NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS GIFU 1051
1gs6 CRYSTAL STRUCTURE OF M144A MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1gs7 CRYSTAL STRUCTURE OF H254F MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1gs8 CRYSTAL STRUCTURE OF M144A MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1hau X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND IN COPPER FREE FORM AT 1.9E RESOLUTION
1haw X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND IN COPPER FREE FORM AT 1.9E RESOLUTION
1ndt NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
1oe1 ATOMIC RESOLUTION STRUCTURE OF THE WILDTYPE NATIVE NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
1oe2 ATOMIC RESOLUTION STRUCTURE OF D92E MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1oe3 ATOMIC RESOLUTION STRUCTURE OF 'HALF APO' NIR
1wa0 CRYSTAL STRUCTURE OF W138H MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1wa1 CRYSTAL STRUCTURE OF H313Q MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1wa2 CRYSTAL STRUCTURE OF H313Q MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE WITH NITRITE BOUND
1wae CRYSTAL STRUCTURE OF H129V MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
2bo0 CRYSTAL STRUCTURE OF THE C130A MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
2bp0 M168L MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS