1NNO - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CONFORMATIONAL CHANGES OCCURRING UPON NO BINDING IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA

Authors :   D. Nurizzo, M. Tegoni, C. Cambillau

Date :   20 Jul 98 (Deposition) - 27 Apr 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

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

Keywords :   Nitrite Reductase, Pseudomonas Aeruginosa, Hemoprotein, Denitrification, No Binding, Conformational Changes, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Nurizzo, F. Cutruzzola, M. Arese, D. Bourgeois, M. Brunori, C. Cambillau, M. Tegoni
Conformational Changes Occurring Upon Reduction And No Binding In Nitrite Reductase From Pseudomonas Aeruginosa.
Biochemistry V. 37 13987 1998
PubMed-ID: 9760233 | Reference-DOI: 10.1021/BI981348Y
(for further references see the PDB file header)

Molecule 1 - NITRITE REDUCTASE
	Atcc	:	NCTC 6750
	Cellular Location	:	PERIPLASMIC SPACE
	Chains	:	A, B
	Collection	:	NCTC 6750
	EC Number	:	1.9.3.2
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Other Details	:	EACH SUBUNIT (A,B) LINKS ONE NITRIC OXIDE (NO) AT THE CATALYTIC SITE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	DHE	2	Ligand/Ion	HEME D
2	HEC	2	Ligand/Ion	HEME C
3	NO	2	Ligand/Ion	NITRIC OXIDE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:46 , CYS A:47 , CYS A:50 , HIS A:51 , LYS A:61 , LEU A:63 , ARG A:71 , TYR A:75 , LEU A:79 , THR A:84 , LEU A:86 , GLY A:87 , MET A:88 , PRO A:89 , TRP A:91 , ALA B:7 , GLU B:8	BINDING SITE FOR RESIDUE HEC A 601
2	AC2	SOFTWARE	ARG A:156 , HIS A:182 , ILE A:183 , ARG A:185 , ARG A:198 , ARG A:225 , SER A:226 , TYR A:245 , ALA A:284 , ILE A:285 , HIS A:327 , ARG A:372 , PHE A:425 , PHE A:441 , GLN A:483 , TRP A:498 , GLY A:531 , PHE A:533 , NO A:603 , HOH A:634 , HOH A:670 , HOH A:711 , HOH A:766 , TYR B:10	BINDING SITE FOR RESIDUE DHE A 602
3	AC3	SOFTWARE	HIS A:327 , HIS A:369 , DHE A:602	BINDING SITE FOR RESIDUE NO A 603
4	AC4	SOFTWARE	GLU A:8 , ARG B:46 , CYS B:47 , CYS B:50 , HIS B:51 , THR B:59 , LYS B:61 , LEU B:63 , ARG B:71 , LEU B:79 , THR B:84 , LEU B:86 , MET B:88 , TRP B:91	BINDING SITE FOR RESIDUE HEC B 601
5	AC5	SOFTWARE	TYR A:10 , ALA A:13 , ARG B:156 , HIS B:182 , ILE B:183 , ARG B:185 , ARG B:198 , ARG B:225 , SER B:226 , TYR B:245 , ALA B:284 , ILE B:285 , HIS B:327 , ARG B:372 , PHE B:425 , PHE B:441 , GLN B:483 , GLY B:531 , PHE B:533 , NO B:603 , HOH B:638 , HOH B:653 , HOH B:679 , HOH B:721	BINDING SITE FOR RESIDUE DHE B 602
6	AC6	SOFTWARE	HIS B:327 , HIS B:369 , DHE B:602	BINDING SITE FOR RESIDUE NO B 603
7	CSA	UNKNOWN	HIS A:327 , HIS A:369 , DHE A:602	CATALYTIC SITE.
8	CSB	UNKNOWN	HIS B:327 , HIS B:369 , DHE B:602	CATALYTIC SITE.

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

Asymmetric/Biological Unit

No.	Residues
1	Trp A:246	-	Pro A:247
2	Trp B:246	-	Pro B:247

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	NIRS_PSEAE	59-138	2	A:34-113 B:34-113

(no "Exon" information available for 1NNO)

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:539
 aligned with NIRS_PSEAE | P24474 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:539
                                    39        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       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559         
           NIRS_PSEAE    30 KAAEQYQGAASAVDPAHVVRTNGAPDMSESEFNEAKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELSKEQITLMAKYIQHTPPQPPEWGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVKVIDTGYAVHISRMSASGRYLLVIGRDARIDMIDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMDGETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKVLLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSKDRRLSALVDVGKTPHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVFDLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSVWNGKNDSSALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDVY 568
               SCOP domains d1nnoa1 A:5-117 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase                                   d1nnoa2 A:118-543 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -1nnoA01 A:6-116 Cytochrome c                                                                                   1nnoA02 A:117-543  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh........hhh...........hhhhhhhhhhhhhh.hhhh.............hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhh..........hhhhhhh......hhh..........hhheeeeeehhh.eeeeee.....eeeeee....eeeeee.....eeeeee...eeeeee......eeeeeee......eeee.........eeeeee....eeeeee.....eeeeee...................eee.....eeeeee....eeeeee.......eeeeee.......eee.....eeeeeehhh.eeeeee....eeeeeee..........eeeee...eeeeeee.....eeeeee............eeeeee................eeeee......hhhh..eeeee........eee.hhhhh.......eee.........eeeeeee.......eeeeee.....eeeee..........eeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------CYTC  PDB: A:34-113 UniProt: 59-138                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nno A   5 KAAEQYQGAASAVDPAHVVRTNGAPDMSESEFNEAKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELSKEQITLMAKYIQHTPPQPPEWGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVKVIDTGYAVHISRMSASGRYLLVIGRDARIDMIDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMDGETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKVLLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSKDRRLSALVDVGKTPHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVFDLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSVWNGKNDSSALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDVY 543
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534

Chain B from PDB  Type:PROTEIN  Length:539
 aligned with NIRS_PSEAE | P24474 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:539
                                    39        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       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559         
           NIRS_PSEAE    30 KAAEQYQGAASAVDPAHVVRTNGAPDMSESEFNEAKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELSKEQITLMAKYIQHTPPQPPEWGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVKVIDTGYAVHISRMSASGRYLLVIGRDARIDMIDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMDGETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKVLLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSKDRRLSALVDVGKTPHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVFDLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSVWNGKNDSSALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDVY 568
               SCOP domains d1nnob1 B:5-117 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase                                   d1nnob2 B:118-543 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -1nnoB01 B:6-116 Cytochrome c                                                                                   1nnoB02 B:117-543  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh........hhh...........hhhhhhhhhhhhhh.hhhh.............hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhh..........hhhhhhh...................hhheeeeeehhh.eeeeee.....eeeeee......eeee.....eeeee....eeeeee......eeeeeee......eeee.........eeeeee....eeeeee.....eeeeee...................eee.....eeeeee....eeeeee.......eeeeee.......eee.....eeeeeehhh.eeeeee....eeeeeee..........eeeee...eeeeeee.....eeeeee............eeeeee................eeeee......hhhh..eeeee........eee.hhhhh.......eee.........eeeeeee.......eeeeee....eeeeee..........eeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------CYTC  PDB: B:34-113 UniProt: 59-138                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nno B   5 KAAEQYQGAASAVDPAHVVRTNGAPDMSESEFNEAKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELSKEQITLMAKYIQHTPPQPPEWGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVKVIDTGYAVHISRMSASGRYLLVIGRDARIDMIDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMDGETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKVLLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSKDRRLSALVDVGKTPHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVFDLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSVWNGKNDSSALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDVY 543
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome Bc1 Complex; Chain D, domain 2 (279)

Homologous Superfamily: Cytochrome c (279)

Pseudomonas aeruginosa. Organism_taxid: 287. (9)

1a	1nnoA01	A:6-116
1b	1nnoB01	B:6-116

Class: Mainly Beta (13760)

Architecture: 8 Propellor (110)

Topology: Methanol Dehydrogenase; Chain A (110)

Homologous Superfamily: [code=2.140.10.20, no name defined] (22)

Pseudomonas aeruginosa. Organism_taxid: 287. (8)

2a	1nnoA02	A:117-543
2b	1nnoB02	B:117-543

(no "Pfam Domain" information available for 1NNO)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NIRS_PSEAE | P24474)

molecular function
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0050418	hydroxylamine reductase activity	Catalysis of the reaction: NH3 + H2O + acceptor = hydroxylamine + reduced acceptor.
	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: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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	Cis Peptide Bonds
		Trp A:246 - Pro A:247	[ RasMol ]
		Trp B:246 - Pro B:247	[ RasMol ]

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	NIRS_PSEAE \| P24474	:	1bl9 1gjq 1hzu 1hzv 1n15 1n50 1n90 1nir

(no "Related Entries Specified in the PDB File" available for 1NNO)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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