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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT (M182T)OF NITRITE REDUCTASE
 
Authors :  H. Guo, K. Olesen, Y. Xue, J. Shapliegh, L. Sjolin
Date :  10 Oct 02  (Deposition) - 28 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Nitrite Reductase, Crystal Structure, Mutant M182T, Gating Mechanism, Electron Transfer, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Guo, K. Olesen, Y. Xue, J. Shapliegh, L. Sjolin
The High Resolution Crystal Structures Of Nitrite Reductase And Its Mutant Met182Thr From Rhodobacter Sphaeroides Reveal A Gating Mechanism For The Electron Transfer To The Type 1 Copper Center
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COPPER-CONTAINING NITRITE REDUCTASE
    Chains: A, B, C
    EC Number: 1.7.99.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 41-371
    Mutation: YES
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063
    Strain: 2.4.3
    Synonym: NITRITE REDUCTASE, CU-NIR

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1CU6Ligand/IonCOPPER (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:126 , CYS A:167 , HIS A:177 , THR A:182BINDING SITE FOR RESIDUE CU A 401
2AC2SOFTWAREASP A:129 , HIS A:131 , HIS A:166 , HOH A:3541 , HIS B:1338BINDING SITE FOR RESIDUE CU A 402
3AC3SOFTWAREHIS B:1126 , CYS B:1167 , HIS B:1177 , THR B:1182BINDING SITE FOR RESIDUE CU B 1401
4AC4SOFTWAREHIS B:1131 , HIS B:1166 , HOH B:3542 , HIS C:2338BINDING SITE FOR RESIDUE CU B 1402
5AC5SOFTWAREHIS C:2126 , CYS C:2167 , HIS C:2177 , THR C:2182BINDING SITE FOR RESIDUE CU C 2401
6AC6SOFTWAREHIS A:338 , ASP C:2129 , HIS C:2131 , HIS C:2166 , HOH C:3543BINDING SITE FOR RESIDUE CU C 2402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MZZ)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Pro A:54 -Pro A:55
2Ile A:99 -Pro A:100
3Pro B:1054 -Pro B:1055
4Ile B:1099 -Pro B:1100
5Pro C:2054 -Pro C:2055
6Ile C:2099 -Pro C:2100

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MZZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MZZ)

(-) Exons   (0, 0)

(no "Exon" information available for 1MZZ)

(-) 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:334
 aligned with NIR_RHOS5 | Q53239 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:334
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368    
           NIR_RHOS5     39 VDLSNLPRVKHTLVPPPFAHAHEQVAASGPVINEFEMRIIEKEVQLDEDAYLQAMTFDGSIPGPLMIVHEGDYVELTLINPPENTMPHNIDFHAATGALGGGGLTLINPGEKVVLRFKATRAGAFVYHCAPGGPMIPWHVVSGMAGCIMVLPRDGLKDHEGKPVRYDTVYYIGESDHYIPKDEDGTYMRFSDPSEGYEDMVAVMDTLIPSHIVFNGAVGALTGEGALKAKVGDNVLFVHSQPNRDSRPHLIGGHGDLVWETGKFHNAPERDLETWFIRGGSAGAALYKFLQPGVYAYVNHNLIEAVHKGATAHVLVEGEWDNDLMEQVVAPVGL  372
               SCOP domains --d1mzza1 A:41-193 Nitrite reductase, NIR                                                                                                                  d1mzza2 A:194-371 Nitrite reductase, NIR                                                                                                                                          - SCOP domains
               CATH domains 1mzzA01 A:39-190 Cupredoxins -  blue copper proteins                                                                                                    1mzzA02 A:191-372 Cupredoxins -  blue copper proteins                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.....................eeeeeeeeeeeeeeee..eeeeeeee.......eeeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee...hhhhhhhhhhh..eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee.....eee.....................eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mzz A   39 VDLSNLPRVKHTLVPPPFAHAHEQVAASGPVINEFEMRIIEKEVQLDEDAYLQAMTFDGSIPGPLMIVHEGDYVELTLINPPENTMPHNIDFHAATGALGGGGLTLINPGEKVVLRFKATRAGAFVYHCAPGGPMIPWHVVSGTAGCIMVLPRDGLKDHEGKPVRYDTVYYIGESDHYIPKDEDGTYMRFSDPSEGYEDMVAVMDTLIPSHIVFNGAVGALTGEGALKAKVGDNVLFVHSQPNRDSRPHLIGGHGDLVWETGKFHNAPERDLETWFIRGGTAGAALYKFLQPGVYAYVNHNLIEAVHKGATAHVLVEGEWDNDLMEQVVAPVGL  372
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368    


Chain B from PDB  Type:PROTEIN  Length:334
 aligned with NIR_RHOS5 | Q53239 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:334
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368    
           NIR_RHOS5     39 VDLSNLPRVKHTLVPPPFAHAHEQVAASGPVINEFEMRIIEKEVQLDEDAYLQAMTFDGSIPGPLMIVHEGDYVELTLINPPENTMPHNIDFHAATGALGGGGLTLINPGEKVVLRFKATRAGAFVYHCAPGGPMIPWHVVSGMAGCIMVLPRDGLKDHEGKPVRYDTVYYIGESDHYIPKDEDGTYMRFSDPSEGYEDMVAVMDTLIPSHIVFNGAVGALTGEGALKAKVGDNVLFVHSQPNRDSRPHLIGGHGDLVWETGKFHNAPERDLETWFIRGGSAGAALYKFLQPGVYAYVNHNLIEAVHKGATAHVLVEGEWDNDLMEQVVAPVGL  372
               SCOP domains --d1mzzb1 B:1041-1193 Nitrite reductase, NIR                                                                                                               d1mzzb2 B:1194-1371 Nitrite reductase, NIR                                                                                                                                        - SCOP domains
               CATH domains 1mzzB01 B:1039-1190 Cupredoxins -  blue copper proteins                                                                                                 1mzzB02 B:1191-1372 Cupredoxins -  blue copper proteins                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.....................eeeeeeeeeeeeeeee..eeeeeeee.......eeeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee...hhhhhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee.....eee.....................eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mzz B 1039 VDLSNLPRVKHTLVPPPFAHAHEQVAASGPVINEFEMRIIEKEVQLDEDAYLQAMTFDGSIPGPLMIVHEGDYVELTLINPPENTMPHNIDFHAATGALGGGGLTLINPGEKVVLRFKATRAGAFVYHCAPGGPMIPWHVVSGTAGCIMVLPRDGLKDHEGKPVRYDTVYYIGESDHYIPKDEDGTYMRFSDPSEGYEDMVAVMDTLIPSHIVFNGAVGALTGEGALKAKVGDNVLFVHSQPNRDSRPHLIGGHGDLVWETGKFHNAPERDLETWFIRGGTAGAALYKFLQPGVYAYVNHNLIEAVHKGATAHVLVEGEWDNDLMEQVVAPVGL 1372
                                  1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228      1238      1248      1258      1268      1278      1288      1298      1308      1318      1328      1338      1348      1358      1368    


Chain C from PDB  Type:PROTEIN  Length:334
 aligned with NIR_RHOS5 | Q53239 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:334
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368    
           NIR_RHOS5     39 VDLSNLPRVKHTLVPPPFAHAHEQVAASGPVINEFEMRIIEKEVQLDEDAYLQAMTFDGSIPGPLMIVHEGDYVELTLINPPENTMPHNIDFHAATGALGGGGLTLINPGEKVVLRFKATRAGAFVYHCAPGGPMIPWHVVSGMAGCIMVLPRDGLKDHEGKPVRYDTVYYIGESDHYIPKDEDGTYMRFSDPSEGYEDMVAVMDTLIPSHIVFNGAVGALTGEGALKAKVGDNVLFVHSQPNRDSRPHLIGGHGDLVWETGKFHNAPERDLETWFIRGGSAGAALYKFLQPGVYAYVNHNLIEAVHKGATAHVLVEGEWDNDLMEQVVAPVGL  372
               SCOP domains --d1mzzc1 C:2041-2193 Nitrite reductase, NIR                                                                                                               d1mzzc2 C:2194-2371 Nitrite reductase, NIR                                                                                                                                        - SCOP domains
               CATH domains 1mzzC01 C:2039-2190 Cupredoxins -  blue copper proteins                                                                                                 1mzzC02 C:2191-2372 Cupredoxins -  blue copper proteins                                                                                                                                CATH domains
           Pfam domains (1) -------------------------------------Cu-oxidase_3-1mzzC04 C:2076-2193                                                                                      ------------Cu-oxidase-1mzzC01 C:2206-2358                                                                                                                           -------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------Cu-oxidase_3-1mzzC05 C:2076-2193                                                                                      ------------Cu-oxidase-1mzzC02 C:2206-2358                                                                                                                           -------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------Cu-oxidase_3-1mzzC06 C:2076-2193                                                                                      ------------Cu-oxidase-1mzzC03 C:2206-2358                                                                                                                           -------------- Pfam domains (3)
         Sec.struct. author .......eee.....................eeeeeeeeeeeeeeee..eeeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee...hhhhhhhhhhh..eeeeeee................eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee.....eee.....................eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mzz C 2039 VDLSNLPRVKHTLVPPPFAHAHEQVAASGPVINEFEMRIIEKEVQLDEDAYLQAMTFDGSIPGPLMIVHEGDYVELTLINPPENTMPHNIDFHAATGALGGGGLTLINPGEKVVLRFKATRAGAFVYHCAPGGPMIPWHVVSGTAGCIMVLPRDGLKDHEGKPVRYDTVYYIGESDHYIPKDEDGTYMRFSDPSEGYEDMVAVMDTLIPSHIVFNGAVGALTGEGALKAKVGDNVLFVHSQPNRDSRPHLIGGHGDLVWETGKFHNAPERDLETWFIRGGTAGAALYKFLQPGVYAYVNHNLIEAVHKGATAHVLVEGEWDNDLMEQVVAPVGL 2372
                                  2048      2058      2068      2078      2088      2098      2108      2118      2128      2138      2148      2158      2168      2178      2188      2198      2208      2218      2228      2238      2248      2258      2268      2278      2288      2298      2308      2318      2328      2338      2348      2358      2368
   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, 6)

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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Clan: CU_oxidase (192)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (NIR_RHOS5 | Q53239)
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:0019333    denitrification pathway    The reduction of nitrate to dinitrogen by four reactions; each intermediate is transformed to the next lower oxidation state; also part of cellular bioenergetics; the nitrogen compounds can serve as terminal acceptors for electron transport phosphorylation in place of oxygen.
    GO:0042128    nitrate assimilation    The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        NIR_RHOS5 | Q53239: 1mzy 1n70 1zv2 2a3t 2dws 2dwt 2dy2

(-) Related Entries Specified in the PDB File

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