1BL9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CONFORMATIONAL CHANGES OCCURRING UPON REDUCTION IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA

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

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

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Nitrite Reductase, Pseudomonas Aeruginosa, Hemoprotein, Denitrification, Domain Swapping, Conformational Changes, Reduction, Oxidoreductase, Electron Transport (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	:	D1 HEME OF SUBUNIT B HAS AN HYDROXIDE ION AS AN AXIAL LIGAND

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	DHE	2	Ligand/Ion	HEME D
2	HEC	2	Ligand/Ion	HEME C
3	OH	1	Ligand/Ion	HYDROXIDE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS B:369 , DHE B:602	BINDING SITE FOR RESIDUE OH B 603
2	AC2	SOFTWARE	ARG A:46 , CYS A:47 , CYS A:50 , HIS A:51 , THR A:59 , GLY A:60 , LYS A:61 , ARG A:71 , LEU A:76 , LEU A:79 , THR A:84 , LEU A:86 , GLY A:87 , MET A:88 , PRO A:89 , TRP A:91 , GLU B:8	BINDING SITE FOR RESIDUE HEC A 601
3	AC3	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:283 , ALA A:284 , ILE A:285 , HIS A:327 , ARG A:372 , PHE A:425 , GLN A:483 , GLY A:531 , PHE A:533 , HOH A:615 , HOH A:634 , TYR B:10	BINDING SITE FOR RESIDUE DHE A 602
4	AC4	SOFTWARE	GLU A:8 , ARG B:46 , CYS B:47 , CYS B:50 , HIS B:51 , GLY B:60 , LYS B:61 , LEU B:63 , ARG B:71 , THR B:84 , LEU B:86 , GLY B:87 , MET B:88 , PRO B:89 , 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:283 , ALA B:284 , ILE B:285 , HIS B:327 , ARG B:372 , PHE B:425 , GLN B:483 , TRP B:498 , GLY B:531 , PHE B:533 , OH B:603 , HOH B:606 , HOH B:609 , HOH B:620	BINDING SITE FOR RESIDUE DHE B 602
6	CSA	UNKNOWN	HIS A:327 , HIS A:369 , DHE A:602	CATALYTIC SITE ON SUBUNIT A
7	CSB	UNKNOWN	HIS B:327 , HIS B:369 , DHE B:602	CATALYTIC SITE ON SUBUNIT B

(no "SS Bond" information available for 1BL9)

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 1BL9)

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 1BL9)

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:537
 aligned with NIRS_PSEAE | P24474 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:537
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       
           NIRS_PSEAE    32 AEQYQGAASAVDPAHVVRTNGAPDMSESEFNEAKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELSKEQITLMAKYIQHTPPQPPEWGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVKVIDTGYAVHISRMSASGRYLLVIGRDARIDMIDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMDGETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKVLLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSKDRRLSALVDVGKTPHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVFDLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSVWNGKNDSSALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDVY 568
               SCOP domains d1bl9a1 A:7-117 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase                                 d1bl9a2 A:118-543 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1bl9A01 A:7-116 Cytochrome c                                                                                  1bl9A02 A:117-543  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhhhh..................hhhhhhh.hhhhhhhhhh................hhhhhhhhhhhh..........hhhhhhh......................eeeeee....eeeeee.....eeeeee....eeeeee.....eeeeee...eeeeee......eeeeeee......eeee.........eeeeee....eeeeee.....eeeeee...................eee.....eeeeee....eeeeee.......eeeeee.......eee.....eeeeee....eeeeee....eeeeeee..........eeeee...eeeeeee.....eeeeee............eeeeee................eeee.............eeeee........eee.............eee.........eeeeeee.......eeeeee....eeeeee..........eee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------CYTC  PDB: A:34-113 UniProt: 59-138                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bl9 A   7 AEQYQGAASAVDPAHVVRTNGAPDMSESEFNEAKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELSKEQITLMAKYIQHTPPQPPEWGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVKVIDTGYAVHISRMSASGRYLLVIGRDARIDMIDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMDGETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKVLLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSKDRRLSALVDVGKTPHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVFDLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSVWNGKNDSSALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDVY 543
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536

Chain B from PDB  Type:PROTEIN  Length:537
 aligned with NIRS_PSEAE | P24474 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:537
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       
           NIRS_PSEAE    32 AEQYQGAASAVDPAHVVRTNGAPDMSESEFNEAKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELSKEQITLMAKYIQHTPPQPPEWGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVKVIDTGYAVHISRMSASGRYLLVIGRDARIDMIDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMDGETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKVLLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSKDRRLSALVDVGKTPHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVFDLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSVWNGKNDSSALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDVY 568
               SCOP domains d1bl9b1 B:7-117 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase                                 d1bl9b2 B:118-543 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1bl9B01 B:7-116 Cytochrome c                                                                                  1bl9B02 B:117-543  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhhhh..................hhhhhhh.hhhhhhhhhh................hhhhhhhhhhhh..........hhhhhhh......................eeeeee....eeeeee.....eeeeee....eeeeee.....eeeeee...eeeeee......eeeeeee......eeee.........eeeeee....eeeeee.....eeeeee...................eee.....eeeeee....eeeeee.......eeeeee.......eee.....eeeeee....eeeeee....eeeeeee..........eeeee...eeeeeee.....eeeeee............eeeeee................eeee.............eeeee........eee.............eee.........eeeeeee.......eeeeee....eeeeee..........eee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------CYTC  PDB: B:34-113 UniProt: 59-138                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bl9 B   7 AEQYQGAASAVDPAHVVRTNGAPDMSESEFNEAKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELSKEQITLMAKYIQHTPPQPPEWGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVTLRDAGQIALVDGDSKKIVKVIDTGYAVHISRMSASGRYLLVIGRDARIDMIDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMDGETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKVLLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSKDRRLSALVDVGKTPHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKNHPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVFDLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSVWNGKNDSSALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDVY 543
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536

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	1bl9A01	A:7-116
1b	1bl9B01	B:7-116

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	1bl9A02	A:117-543
2b	1bl9B02	B:117-543

(no "Pfam Domain" information available for 1BL9)

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

(no "Related Entries Specified in the PDB File" available for 1BL9)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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