1L9R - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE I257M VARIANT OF THE COPPER-CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIS S-6

Authors :   M. J. Boulanger, M. E. P. Murphy

Date :   26 Mar 02 (Deposition) - 04 Feb 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.78

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Cupredoxin Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Boulanger, M. E. P. Murphy
Directing The Mode Of Nitrite Binding To A Copper-Containing Nitrite Reductase From Alcaligenes Faecalis S-6: Characterization Of An Active Site Isoleucine
Protein Sci. V. 12 248 2003
PubMed-ID: 12538888 | Reference-DOI: 10.1110/PS.0224503
(for further references see the PDB file header)

Molecule 1 - COPPER-CONTAINING NITRITE REDUCTASE
	Chains	:	A, B, C
	EC Number	:	1.7.99.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	HMS174DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 40-376
	Gene	:	NIRK
	Mutation	:	YES
	Organism Scientific	:	ALCALIGENES FAECALIS
	Organism Taxid	:	511
	Synonym	:	CU-NIR

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 9)

No.	Name	Count	Type	Full Name
1	CU	6	Ligand/Ion	COPPER (II) ION
2	NO2	3	Ligand/Ion	NITRITE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:95 , CYS A:136 , HIS A:145 , MET A:150	BINDING SITE FOR RESIDUE CU A 501
2	AC2	SOFTWARE	HIS A:100 , HIS A:135 , HIS B:306 , NO2 B:504 , HOH B:6003	BINDING SITE FOR RESIDUE CU A 502
3	AC3	SOFTWARE	HIS A:135 , CU A:502 , MET B:257 , VAL B:304 , HIS B:306 , LEU B:308 , HOH B:6003	BINDING SITE FOR RESIDUE NO2 B 504
4	AC4	SOFTWARE	HIS B:95 , CYS B:136 , HIS B:145 , MET B:150	BINDING SITE FOR RESIDUE CU B 501
5	AC5	SOFTWARE	HIS B:100 , HIS B:135 , HIS C:306 , NO2 C:604 , HOH C:6006	BINDING SITE FOR RESIDUE CU B 502
6	AC6	SOFTWARE	HIS B:135 , CU B:502 , HIS C:255 , MET C:257 , HIS C:306 , LEU C:308 , HOH C:6006	BINDING SITE FOR RESIDUE NO2 C 604
7	AC7	SOFTWARE	HIS C:95 , CYS C:136 , HIS C:145 , MET C:150	BINDING SITE FOR RESIDUE CU C 501
8	AC8	SOFTWARE	HIS A:306 , NO2 A:704 , HIS C:100 , HIS C:135	BINDING SITE FOR RESIDUE CU C 502
9	AC9	SOFTWARE	HIS A:255 , MET A:257 , HIS A:306 , ASP C:98 , HIS C:135 , CU C:502	BINDING SITE FOR RESIDUE NO2 A 704

(no "SS Bond" information available for 1L9R)

Asymmetric/Biological Unit

No.	Residues
1	Pro A:22	-	Pro A:23
2	Val A:68	-	Pro A:69
3	Pro B:22	-	Pro B:23
4	Val B:68	-	Pro B:69
5	Pro C:22	-	Pro C:23
6	Val C:68	-	Pro C:69

(no "SAP(SNP)/Variant" information available for 1L9R)

(no "PROSITE Motif" information available for 1L9R)

(no "Exon" information available for 1L9R)

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:336
 aligned with NIR_ALCFA | P38501 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:336
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369      
            NIR_ALCFA    40 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 375
               SCOP domains d1l9ra1 A:4-166 Nitrite reductase, NIR                                                                                                                             d1l9ra2 A:167-339 Nitrite reductase, NIR                                                                                                                                      SCOP domains
               CATH domains -------1l9rA01 A:11-158 Cupredoxins -  blue copper proteins                                                                                                1l9rA02 A:159-325 Cupredoxins -  blue copper proteins                                                                                                                  -------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhh..eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1l9r A   4 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLMGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 339
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333

Chain B from PDB  Type:PROTEIN  Length:336
 aligned with NIR_ALCFA | P38501 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:336
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369      
            NIR_ALCFA    40 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 375
               SCOP domains d1l9rb1 B:4-166 Nitrite reductase, NIR                                                                                                                             d1l9rb2 B:167-339 Nitrite reductase, NIR                                                                                                                                      SCOP domains
               CATH domains -------1l9rB01 B:11-158 Cupredoxins -  blue copper proteins                                                                                                1l9rB02 B:159-325 Cupredoxins -  blue copper proteins                                                                                                                  -------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1l9r B   4 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLMGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 339
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333

Chain C from PDB  Type:PROTEIN  Length:336
 aligned with NIR_ALCFA | P38501 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:336
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369      
            NIR_ALCFA    40 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 375
               SCOP domains d1l9rc1 C:4-166 Nitrite reductase, NIR                                                                                                                             d1l9rc2 C:167-339 Nitrite reductase, NIR                                                                                                                                      SCOP domains
               CATH domains -------1l9rC01 C:11-158 Cupredoxins -  blue copper proteins                                                                                                1l9rC02 C:159-325 Cupredoxins -  blue copper proteins                                                                                                                  -------------- CATH domains
           Pfam domains (1) ----------------------------------------Cu-oxidase_3-1l9rC04 C:44-161                                                                                         ------------Cu-oxidase-1l9rC01 C:174-326                                                                                                                             ------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------Cu-oxidase_3-1l9rC05 C:44-161                                                                                         ------------Cu-oxidase-1l9rC02 C:174-326                                                                                                                             ------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------Cu-oxidase_3-1l9rC06 C:44-161                                                                                         ------------Cu-oxidase-1l9rC03 C:174-326                                                                                                                             ------------- Pfam domains (3)
         Sec.struct. author .hhhhhhh..eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1l9r C   4 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLMGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 339
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: Multidomain cupredoxins (146)

Protein domain: Nitrite reductase, NIR (79)

Alcaligenes faecalis, strain s-6 [TaxId: 511] (31)

1a	d1l9ra1	A:4-166
1b	d1l9ra2	A:167-339
1c	d1l9rb1	B:4-166
1d	d1l9rb2	B:167-339
1e	d1l9rc1	C:4-166
1f	d1l9rc2	C:167-339

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Cupredoxins - blue copper proteins (420)

Alcaligenes faecalis. Organism_taxid: 511. (13)

1a	1l9rA01	A:11-158
1b	1l9rB01	B:11-158
1c	1l9rC01	C:11-158
1d	1l9rA02	A:159-325
1e	1l9rB02	B:159-325
1f	1l9rC02	C:159-325

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Cu-oxidase (74)

Alcaligenes faecalis (18)

1a	Cu-oxidase-1l9rC01	C:174-326
1b	Cu-oxidase-1l9rC02	C:174-326
1c	Cu-oxidase-1l9rC03	C:174-326

Family: Cu-oxidase_3 (79)

Alcaligenes faecalis (18)

2a	Cu-oxidase_3-1l9rC04	C:44-161
2b	Cu-oxidase_3-1l9rC05	C:44-161
2c	Cu-oxidase_3-1l9rC06	C:44-161

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (NIR_ALCFA | P38501)

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).

Asymmetric/Biological Unit
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		Pro A:22 - Pro A:23	[ RasMol ]
		Pro B:22 - Pro B:23	[ RasMol ]
		Pro C:22 - Pro C:23	[ RasMol ]
		Val A:68 - Pro A:69	[ RasMol ]
		Val B:68 - Pro B:69	[ RasMol ]
		Val C:68 - Pro C:69	[ RasMol ]

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1l9o	CRYSTAL STRUCTURE OF NITRITE SOAKED I257A VARIANT OF THE COPPER-CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIS
1l9p	CRYSTAL STRUCTURE OF NITRITE SOAKED I257G VARIANT OF THE COPPER-CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIES S-6
1l9q	CRYSTAL STRUCTURE OF THE I257L VARIANT OF THE COPPER- CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIS S-6
1l9s	CRYSTAL STRUCTURE OF THE I257T VARIANT OF THE COPPER- CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIS S-6
1l9t	CRYSTAL STRUCTURE OF THE I257V VARIANT OF THE COPPER- CONTAINING NITRITE REDUCTASE FROM ALCALIGENES FAECALIS S-6

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 6)

CATH Domains (1, 6)

Pfam Domains (2, 6)

Gene Ontology (9, 9)

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