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(-) Description

Title :  TYPE 1 COPPER-BINDING LOOP OF NITRITE REDUCTASE MUTANT: 130-CAPEGMVPWHVVSGM-144 TO 130-CTPHPFM-136
 
Authors :  K. Sato, S. J. Firbank, C. Li, M. J. Banfield, C. Dennison
Date :  28 Jan 08  (Deposition) - 23 Dec 08  (Release) - 23 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Cupredoxin, Type 1 Copper, Type 2 Copper, Electron Transfer, Loop-Directed Mutagenesis, Copper-Containing Nitrite Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Sato, S. J. Firbank, C. Li, M. J. Banfield, C. Dennison
The Importance Of The Long Type 1 Copper-Binding Loop Of Nitrite Reductase For Structure And Function.
Chemistry V. 14 5820 2008
PubMed-ID: 18491346  |  Reference-DOI: 10.1002/CHEM.200701997

(-) Compounds

Molecule 1 - DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: RESIDUES 25-154,168-360
    Organism Scientific: ALCALIGENES XYLOSOXYDANS XYLOSOXYDANS
    Organism Taxid: 85698
    Synonym: NITRITE REDUCTASE, NIR, NITRITE REDUCTASE LOOP MUTANT

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
2ZN3Ligand/IonZINC ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1EPE3Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:92 , HIS A:94 , HIS A:129 , HIS A:292 , HOH A:2088BINDING SITE FOR RESIDUE ZN A1328
2AC2SOFTWAREHIS A:157 , ASP A:159 , GLU A:187 , HOH A:2089BINDING SITE FOR RESIDUE ZN A1329
3AC3SOFTWAREHIS A:89 , CYS A:130 , HIS A:133 , MET A:136 , HOH A:2090BINDING SITE FOR RESIDUE ZN A1330
4AC4SOFTWAREASP A:47 , ASP A:48 , LYS A:49 , PHE A:298 , GLU A:299BINDING SITE FOR RESIDUE EPE A1331

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VMJ)

(-) 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:326
 aligned with O68601_ALCXX | O68601 from UniProtKB/TrEMBL  Length:360

    Alignment length:334
                                    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 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIP 359
               SCOP domains d2vmja1 A:2-151 automated matches                                                                                                                             d2vmja2 A:152-327 automated matches                                                                                                                                              SCOP domains
               CATH domains 2vmjA01 A:2-144 Cupredoxins -  blue copper proteins                                                                                                    2vmjA02 A:145-311 Cupredoxins -  blue copper proteins                                                                                                                  ---------------- CATH domains
               Pfam domains ------------------------------------Cu-oxidase_3-2vmjA02 A:38-147                                                                   ---  -----            ------------Cu-oxidase-2vmjA01 A:160-312                                                                                                                             --------------- Pfam domains
         Sec.struct. author ......eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeeee..e---ee-----eeeeeeee................eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vmj A   2 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCTPH---PF-----MSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIP 327
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 |   ||  -  |    143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323    
                                                                                                                                                             133 134|   136                                                                                                                                                                                               
                                                                                                                                                                  135
   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  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: CU_oxidase (192)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (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 | O68601: 1bq5 1gs6 1gs7 1gs8 1hau 1haw 1ndt 1oe1 1oe2 1oe3 1wa0 1wa1 1wa2 1wae 2bo0 2bp0 2bp8 2jfc 2vm3 2vm4 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 M144L MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
2bp8 M144Q STRUCTURE OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
2jfc M144L MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS IN SPACE GROUP P212121
2vm3 STRUCTURE OF ALCALIGENES XYLOSOXIDANS IN SPACE GROUP R3 - 1 OF 2
2vm4 STRUCTURE OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE IN SPACE GROUP R3 - 2 OF 2