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PR00695

Identifier
CUNO2RDTASE  [View Relations]  [View Alignment]  
Accession
PR00695
No. of Motifs
6
Creation Date
12-APR-1997  (UPDATE 07-JUN-1999)
Title
Copper containing nitrite reductase signature
Database References

INTERPRO; IPR001287
PDB; 2NRD
SCOP; 2NRD
CATH; 2NRD
Literature References
1. GODDEN, J.W., TURLEY, S., TELLER, D.C., ADMAN, E.T., LIU, M.Y.,
PAYNE, W.J. AND LEGALL, J.
The 2.3 Angstrom X-ray structure of nitrite reductase from Achromobacter
cycloclastes.
SCIENCE 253 438-442 (1991).

Documentation
The 3D structure of the copper-containing nitrite reductase (NIR) from
Achromobacter cycloclastes has been determined to 2.3A resolution [1]. The
enzyme is a trimer, each monomer of which contains two Greek key beta-barrel
domains (similar to that of plastocyanin) and houses two copper sites. The
two copper atoms in the monomer comprise one type I copper site (Cu-I:
two His, one Cys and one Met ligand) and one putative type II copper site
(Cu-II: three His and one solvent ligand) [1]. Although ligated by adjacent
amino acids, Cu-I and Cu-II are ~12.5A apart. Cu-II is bound with near
perfect tetrahedral geometry by residues from each of two monomers [1].
The Cu-II site lies at the bottom of a 12A deep solvent channel and is the
site to which the substrate (NO2-) binds [1].
 
CUNO2RDTASE is a 6-element fingerprint that provides a signature for
copper-containing nitrite reductases. The fingerprint was derived from an
initial alignment of 6 sequences: the motifs were drawn from short conserved
regions spanning the full alignment length - motif 1 spans the second 
strand; motif 2 encompasses strand 4; motif 3 spans strand 5; motif 4 
includes helix 1; motif 5 spans strand 8; and motif 6 spans helix 2 and
strand 9. Two iterations on OWL29.2 were required to reach convergence,
at which point a true set comprising 8 sequences was identified.
 
An update on SPTR37_9f identified a true set of 9 sequences.
Summary Information
9 codes involving  6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
6999999
5000000
4000000
3000000
2000000
123456
True Positives
ANIA_NEIGO    NIR_ACHCY     NIR_ALCFA     NIR_PSEAR     
NIR_PSESP NIR_RHIHE NIR_RHOSH O31380
O68601
Sequence Titles
ANIA_NEIGO  MAJOR OUTER MEMBRANE PROTEIN PAN 1 PRECURSOR - NEISSERIA GONORRHOEAE. 
NIR_ACHCY COPPER-CONTAINING NITRITE REDUCTASE PRECURSOR (EC 1.7.99.3) (CU-NIR) - ACHROMOBACTER CYCLOCLASTES.
NIR_ALCFA COPPER-CONTAINING NITRITE REDUCTASE PRECURSOR (EC 1.7.99.3) (CU-NIR) - ALCALIGENES FAECALIS.
NIR_PSEAR COPPER-CONTAINING NITRITE REDUCTASE PRECURSOR (EC 1.7.99.3) (CU-NIR) - PSEUDOMONAS AUREOFACIENS.
NIR_PSESP COPPER-CONTAINING NITRITE REDUCTASE PRECURSOR (EC 1.7.99.3) (CU-NIR) - PSEUDOMONAS SP. (STRAIN G-179).
NIR_RHIHE COPPER-CONTAINING NITRITE REDUCTASE PRECURSOR (EC 1.7.99.3) (CU-NIR) - RHIZOBIUM HEDYSARI.
NIR_RHOSH COPPER-CONTAINING NITRITE REDUCTASE PRECURSOR (EC 1.7.99.3) (CU-NIR) - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
O31380 RESPIRATORY NITRITE REDUCTASE - BRADYRHIZOBIUM JAPONICUM.
O68601 DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE - ALCALIGENES XYLOSOXYDANS XYLOSOXYDANS (ACHROMOBACTER XYLOSOXIDANS).
Scan History
OWL29_2    2  50   NSINGLE    
SPTR37_9f 2 10 NSINGLE
Initial Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
PRVVEFTMTIEEKKLVIDR NIR_ACHCY 36 36 -
PKVVEFKMTIQEKKIVVDD NIR_PSESP 75 75 -
PKVVEFTMVIEEKKIVIDD NIR_ALCFA 72 72 -
PKVVQFRMSIEEKKMVIDD NIR_PSEAR 54 54 -
PAKVRVKMETVEKTMKMDD ANIA_NEIGO 76 76 -

Motif 2 width=17
Element Seqn Id St Int Rpt
TFNGSVPGPLMVVHEND NIR_ACHCY 63 8 -
TFDGSVPGPMMIVHQDD NIR_PSESP 102 8 -
AFNGTVPGPLMVVHQDD NIR_ALCFA 99 8 -
TFNGSMPGPTLVVHEGD NIR_PSEAR 81 8 -
TFDGDVPGRMIRVREGD ANIA_NEIGO 102 7 -

Motif 3 width=18
Element Seqn Id St Int Rpt
VELRLINPDTNTLLHNID NIR_ACHCY 81 1 -
VELTLVNPDTNELQHNID NIR_PSESP 120 1 -
LELTLINPETNTLMHNID NIR_ALCFA 117 1 -
IELTLVNPATNSMPHNVD NIR_PSEAR 99 1 -
VEVEFSNNPSSTVPHNVD ANIA_NEIGO 120 1 -

Motif 4 width=20
Element Seqn Id St Int Rpt
DFHAATGALGGGALTQVNPG NIR_ACHCY 98 -1 -
DFHSATGALGGGALTVVNPG NIR_PSESP 137 -1 -
DFHAATGALGGGGLTEINPG NIR_ALCFA 134 -1 -
DFHAATGALGGAGLTQVVPG NIR_PSEAR 116 -1 -
DFHAATGQGGGAAATFTAPG ANIA_NEIGO 137 -1 -

Motif 5 width=16
Element Seqn Id St Int Rpt
RFKATKPGVFVYHCAP NIR_ACHCY 123 5 -
RFKATKAGVFVYHCAP NIR_PSESP 162 5 -
RFKATKPGVFVYHCAP NIR_ALCFA 159 5 -
RFKADRSGTFVYHCAP NIR_PSEAR 141 5 -
SFKALQPGLYIYHCAV ANIA_NEIGO 162 5 -

Motif 6 width=17
Element Seqn Id St Int Rpt
MVPWHVTSGMNGAIMVL NIR_ACHCY 141 2 -
MVPWHVTSGMNGAIMVL NIR_PSESP 180 2 -
MVPWHVVSGMNGAIMVL NIR_ALCFA 177 2 -
MVPWHVVSGMNGALMVL NIR_PSEAR 159 2 -
PVGMHIANGMYGLILVE ANIA_NEIGO 179 1 -
Final Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
PRVVEFTMTIEEKKLVIDR NIR_ACHCY 36 36 -
PKVVEVTLTIEEKKLVIDG NIR_RHIHE 73 73 -
PKVVEFKMTIQEKKIVVDD NIR_PSESP 75 75 -
PKVVEFTMVIEEKKIVIDD NIR_ALCFA 72 72 -
PKIVEFKLTIEEKKVVIDE O31380 54 54 -
PKVVEFTMTIEEKKMVIDD O68601 54 54 -
PKVVQFRMSIEEKKMVIDD NIR_PSEAR 54 54 -
PVINEFEMRIIEKEVQLDE NIR_RHOSH 68 68 -
PAKVRVKMETVEKTMKMDD ANIA_NEIGO 76 76 -

Motif 2 width=17
Element Seqn Id St Int Rpt
TFNGSVPGPLMVVHEND NIR_ACHCY 63 8 -
TFDGSVPGPLIVVHQDD NIR_RHIHE 100 8 -
TFDGSVPGPMMIVHQDD NIR_PSESP 102 8 -
AFNGTVPGPLMVVHQDD NIR_ALCFA 99 8 -
TFNGSMPGPLMVVHEGD O31380 81 8 -
TFNGSMPGPTLVVHEGD O68601 81 8 -
TFNGSMPGPTLVVHEGD NIR_PSEAR 81 8 -
TFDGSIPGPLMIVHEGD NIR_RHOSH 94 7 -
TFDGDVPGRMIRVREGD ANIA_NEIGO 102 7 -

Motif 3 width=18
Element Seqn Id St Int Rpt
VELRLINPDTNTLLHNID NIR_ACHCY 81 1 -
VEVTLVNPETNTLQHNID NIR_RHIHE 118 1 -
VELTLVNPDTNELQHNID NIR_PSESP 120 1 -
LELTLINPETNTLMHNID NIR_ALCFA 117 1 -
VETTLVNPATNTMPHNID O31380 99 1 -
VQLTLVNPATNAMPHNVD O68601 99 1 -
IELTLVNPATNSMPHNVD NIR_PSEAR 99 1 -
VELTLINPPENTMPHNID NIR_RHOSH 112 1 -
VEVEFSNNPSSTVPHNVD ANIA_NEIGO 120 1 -

Motif 4 width=20
Element Seqn Id St Int Rpt
DFHAATGALGGGALTQVNPG NIR_ACHCY 98 -1 -
DFHSATGALGGGALTVVNPG NIR_RHIHE 135 -1 -
DFHSATGALGGGALTVVNPG NIR_PSESP 137 -1 -
DFHAATGALGGGGLTEINPG NIR_ALCFA 134 -1 -
DFHSATGALGGGALTLINPG O31380 116 -1 -
DFHGATGALGGAKLTNVNPG O68601 116 -1 -
DFHAATGALGGAGLTQVVPG NIR_PSEAR 116 -1 -
DFHAATGALGGGGLTLINPG NIR_RHOSH 129 -1 -
DFHAATGQGGGAAATFTAPG ANIA_NEIGO 137 -1 -

Motif 5 width=16
Element Seqn Id St Int Rpt
RFKATKPGVFVYHCAP NIR_ACHCY 123 5 -
RFKATKAGVFVYHCAP NIR_RHIHE 160 5 -
RFKATKAGVFVYHCAP NIR_PSESP 162 5 -
RFKATKPGVFVYHCAP NIR_ALCFA 159 5 -
RWKATKTGVFVYHCAP O31380 141 5 -
RFKADRSGTFVYHCAP O68601 141 5 -
RFKADRSGTFVYHCAP NIR_PSEAR 141 5 -
RFKATRAGAFVYHCAP NIR_RHOSH 154 5 -
SFKALQPGLYIYHCAV ANIA_NEIGO 162 5 -

Motif 6 width=17
Element Seqn Id St Int Rpt
MVPWHVTSGMNGAIMVL NIR_ACHCY 141 2 -
MVPWHVTSGMNGAIMVL NIR_RHIHE 178 2 -
MVPWHVTSGMNGAIMVL NIR_PSESP 180 2 -
MVPWHVVSGMNGAIMVL NIR_ALCFA 177 2 -
MIPWHVVSGMNGAVMVL O31380 160 3 -
MVPWHVVSGMSGTLMVL O68601 159 2 -
MVPWHVVSGMNGALMVL NIR_PSEAR 159 2 -
MIPWHVVSGMAGCIMVL NIR_RHOSH 173 3 -
PVGMHIANGMYGLILVE ANIA_NEIGO 179 1 -