3SBQ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   PSEUDOMONAS STUTZERI NITROUS OXIDE REDUCTASE, P65 CRYSTAL FORM

Authors :   A. Pomowski, W. G. Zumft, P. M. H. Kroneck, O. Einsle

Date :   06 Jun 11 (Deposition) - 10 Aug 11 (Release) - 21 Sep 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Beta-Propeller, Cupredoxin Domain, Reductase, Copper-Containing, Periplasmic, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Pomowski, W. G. Zumft, P. M. Kroneck, O. Einsle
N2O Binding At A [4Cu:2S] Copper-Sulphur Cluster In Nitrous Oxide Reductase.
Nature V. 477 234 2011
PubMed-ID: 21841804 | Reference-DOI: 10.1038/NATURE10332

Molecule 1 - NITROUS-OXIDE REDUCTASE
	Chains	:	A, B
	EC Number	:	1.7.99.6
	Organism Common	:	PSEUDOMONAS PERFECTOMARINA
	Organism Scientific	:	PSEUDOMONAS STUTZERI
	Organism Taxid	:	316
	Synonym	:	N(2)OR, N2O REDUCTASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 11)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	CL	2	Ligand/Ion	CHLORIDE ION
3	CUA	2	Ligand/Ion	DINUCLEAR COPPER ION
4	CUK	2	Ligand/Ion	[4CU:2S] CLUSTER
5	IMD	1	Ligand/Ion	IMIDAZOLE
6	K	2	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:583 , CYS A:618 , TRP A:620 , CYS A:622 , HIS A:626 , MET A:629	BINDING SITE FOR RESIDUE CUA A 701
02	AC2	SOFTWARE	HIS A:129 , HIS A:130 , HIS A:178 , HIS A:326 , HIS A:382 , HIS A:433 , HIS A:494 , PHE B:621	BINDING SITE FOR RESIDUE CUK A 702
03	AC3	SOFTWARE	LYS A:454 , GLU A:469 , HOH A:794 , HOH A:879 , HOH B:737 , HOH B:824	BINDING SITE FOR RESIDUE K A 705
04	AC4	SOFTWARE	TYR A:256 , GLU A:259 , MET A:267 , ASP A:273 , ASN A:324 , HOH A:973	BINDING SITE FOR RESIDUE CA A 703
05	AC5	SOFTWARE	ARG A:181 , ASN A:241 , CYS A:328 , ASN A:329 , HIS A:382	BINDING SITE FOR RESIDUE CL A 704
06	AC6	SOFTWARE	TYR B:256 , GLU B:259 , MET B:267 , ASP B:273 , ASN B:324 , HOH B:890	BINDING SITE FOR RESIDUE CA B 703
07	AC7	SOFTWARE	ARG B:181 , GLY B:327 , CYS B:328 , ASN B:329 , HIS B:382	BINDING SITE FOR RESIDUE CL B 704
08	AC8	SOFTWARE	CYS B:618 , TRP B:620 , CYS B:622 , HIS B:626 , MET B:629	BINDING SITE FOR RESIDUE CUA B 701
09	AC9	SOFTWARE	PHE A:621 , HIS B:129 , HIS B:130 , HIS B:178 , HIS B:326 , HIS B:382 , HIS B:433 , HIS B:494	BINDING SITE FOR RESIDUE CUK B 702
10	BC1	SOFTWARE	HOH A:985 , LYS B:454 , GLU B:469 , HOH B:644 , HOH B:831	BINDING SITE FOR RESIDUE K B 705
11	BC2	SOFTWARE	TRP A:615 , GLU B:196 , PHE B:197 , ILE B:198 , ASN B:238 , TYR B:256 , ASN B:257 , MET B:267 , HOH B:719	BINDING SITE FOR RESIDUE IMD B 639

(no "SS Bond" information available for 3SBQ)

Asymmetric/Biological Unit

No.	Residues
1	Val A:87	-	Pro A:88
2	Val A:185	-	Pro A:186
3	His A:201	-	Pro A:202
4	Pro A:322	-	Lys A:323
5	His A:428	-	Tyr A:429
6	Ala A:552	-	Pro A:553
7	Val B:87	-	Pro B:88
8	Val B:185	-	Pro B:186
9	His B:201	-	Pro B:202
10	Pro B:322	-	Lys B:323
11	His B:428	-	Tyr B:429
12	Ala B:552	-	Pro B:553

(no "SAP(SNP)/Variant" information available for 3SBQ)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COX2_CUA	PS50857	Cytochrome oxidase subunit II copper A binding domain profile.	NOSZ_PSEST	539-638	2	A:539-638 B:539-638
2	COX2	PS00078	CO II and nitrous oxide reductase dinuclear copper centers signature.	NOSZ_PSEST	581-629	2	A:581-629 B:581-629

(no "Exon" information available for 3SBQ)

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:581
 aligned with NOSZ_PSEST | P19573 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:581
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637 
           NOSZ_PSEST    58 QKIHVGPGELDDYYGFWSGGHQGEVRVLGVPSMRELMRIPVFNVDSATGWGLTNESRHIMGDSAKFLNGDCHHPHISMTDGKYDGKYLFINDKANSRVARIRLDIMKCDKMITVPNVQAIHGLRLQKVPHTKYVFANAEFIIPHPNDGKVFDLQDENSYTMYNAIDAETMEMAFQVIVDGNLDNTDADYTGRFAAATCYNSEKAFDLGGMMRNERDWVVVFDIHAVEAAVKAGDFITLGDSKTPVLDGRKKDGKDSKFTRYVPVPKNPHGCNTSSDGKYFIAAGKLSPTCSMIAIDKLPDLFAGKLADPRDVIVGEPELGLGPLHTTFDGRGNAYTTLFIDSQVVKWNMEEAVRAYKGEKVNYIKQKLDVHYQPGHLHASLCETNEADGKWLVALSKFSKDRFLPVGPLHPENDQLIDISGDEMKLVHDGPTFAEPHDCIMARRDQIKTKKIWDRNDPFFAPTVEMAKKDGINLDTDNKVIRDGNKVRVYMTSMAPAFGVQEFTVKQGDEVTVTITNIDQIEDVSHGFVVVNHGVSMEISPQQTSSITFVADKPGLHWYYCSWFCHALHMEMVGRMMVEPA 638
               SCOP domains d3sbqa1 A:58-507 automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                d3sbqa2 A:508-638 automated matches                                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee.hhhh.eeeeee...eeeeee.............hhhhhhhhhhhhhh........eeeee..eeeeeeeeeee....eeeeee....eeeeeee......eeeeee.......eeeeee...ee..............eeeeeeeee.....eeeeeee......eee.....eeeeee.......hhhhhh....eeeeeeehhhhhhhhhhh...........eee...........eeeeee......eee.....eeeee......eeeee..hhhhhhh....hhhh.eee.......eeeeee....eeeeee....eeeeeehhhhhhhhh......eeeeee....eeeeee...........eeeeee...............eeeeeee......eeeeeeee......eeeee.hhh.........hhhhhhhhhhhhhh........eeeee..eeeeeeeee..ee...eeeee...eeeeeeee........eeeee....eeeee....eeeeeee....eeeeee............eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX2_CUA  PDB: A:539-638 UniProt: 539-638                                                            PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX2  PDB: A:581-629 UniProt: 581-629            --------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sbq A  58 QKIHVGPGELDDYYGFWSGGHQGEVRVLGVPSMRELMRIPVFNVDSATGWGLTNESRHIMGDSAKFLNGDCHHPHISMTDGKYDGKYLFINDKANSRVARIRLDIMKCDKMITVPNVQAIHGLRLQKVPHTKYVFANAEFIIPHPNDGKVFDLQDENSYTMYNAIDAETMEMAFQVIVDGNLDNTDADYTGRFAAATCYNSEKAFDLGGMMRNERDWVVVFDIHAVEAAVKAGDFITLGDSKTPVLDGRKKDGKDSKFTRYVPVPKNPHGCNTSSDGKYFIAAGKLSPTCSMIAIDKLPDLFAGKLADPRDVIVGEPELGLGPLHTTFDGRGNAYTTLFIDSQVVKWNMEEAVRAYKGEKVNYIKQKLDVHYQPGHLHASLCETNEADGKWLVALSKFSKDRFLPVGPLHPENDQLIDISGDEMKLVHDGPTFAEPHDCIMARRDQIKTKKIWDRNDPFFAPTVEMAKKDGINLDTDNKVIRDGNKVRVYMTSMAPAFGVQEFTVKQGDEVTVTITNIDQIEDVSHGFVVVNHGVSMEISPQQTSSITFVADKPGLHWYYCSWFCHALHMEMVGRMMVEPA 638
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637

Chain B from PDB  Type:PROTEIN  Length:581
 aligned with NOSZ_PSEST | P19573 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:581
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637 
           NOSZ_PSEST    58 QKIHVGPGELDDYYGFWSGGHQGEVRVLGVPSMRELMRIPVFNVDSATGWGLTNESRHIMGDSAKFLNGDCHHPHISMTDGKYDGKYLFINDKANSRVARIRLDIMKCDKMITVPNVQAIHGLRLQKVPHTKYVFANAEFIIPHPNDGKVFDLQDENSYTMYNAIDAETMEMAFQVIVDGNLDNTDADYTGRFAAATCYNSEKAFDLGGMMRNERDWVVVFDIHAVEAAVKAGDFITLGDSKTPVLDGRKKDGKDSKFTRYVPVPKNPHGCNTSSDGKYFIAAGKLSPTCSMIAIDKLPDLFAGKLADPRDVIVGEPELGLGPLHTTFDGRGNAYTTLFIDSQVVKWNMEEAVRAYKGEKVNYIKQKLDVHYQPGHLHASLCETNEADGKWLVALSKFSKDRFLPVGPLHPENDQLIDISGDEMKLVHDGPTFAEPHDCIMARRDQIKTKKIWDRNDPFFAPTVEMAKKDGINLDTDNKVIRDGNKVRVYMTSMAPAFGVQEFTVKQGDEVTVTITNIDQIEDVSHGFVVVNHGVSMEISPQQTSSITFVADKPGLHWYYCSWFCHALHMEMVGRMMVEPA 638
               SCOP domains d3sbqb1 B:58-507 automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                d3sbqb2 B:508-638 automated matches                                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee.hhhh.eeeeee...eeeeee.............hhhhhhhhhhhhhh........eeeee..eeeeeeeeeee....eeeeee....eeeeeee......eeeeee.......eeeeee...ee..............eeeeeeeee.....eeeeeee......eee.....eeeeee.......hhhhhh....eeeeeeehhhhhhhhhhh...........eee...........eeeeee......eee.....eeeee......eeeee..hhhhhhh....hhhh.eee.......eeeeee....eeeeee....eeeeeehhhhhhhhh......eeeeee....eeeeee...........eeeeee...............eeeeeee......eeeeeeee......eeeee.hhh............hhhhhhhhhhh........eeeee..eeeeeeeee..ee...eeeee...eeeeeeee........eeeee....eeeee....eeeeeee....eeeeee.......hhhh.eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX2_CUA  PDB: B:539-638 UniProt: 539-638                                                            PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COX2  PDB: B:581-629 UniProt: 581-629            --------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sbq B  58 QKIHVGPGELDDYYGFWSGGHQGEVRVLGVPSMRELMRIPVFNVDSATGWGLTNESRHIMGDSAKFLNGDCHHPHISMTDGKYDGKYLFINDKANSRVARIRLDIMKCDKMITVPNVQAIHGLRLQKVPHTKYVFANAEFIIPHPNDGKVFDLQDENSYTMYNAIDAETMEMAFQVIVDGNLDNTDADYTGRFAAATCYNSEKAFDLGGMMRNERDWVVVFDIHAVEAAVKAGDFITLGDSKTPVLDGRKKDGKDSKFTRYVPVPKNPHGCNTSSDGKYFIAAGKLSPTCSMIAIDKLPDLFAGKLADPRDVIVGEPELGLGPLHTTFDGRGNAYTTLFIDSQVVKWNMEEAVRAYKGEKVNYIKQKLDVHYQPGHLHASLCETNEADGKWLVALSKFSKDRFLPVGPLHPENDQLIDISGDEMKLVHDGPTFAEPHDCIMARRDQIKTKKIWDRNDPFFAPTVEMAKKDGINLDTDNKVIRDGNKVRVYMTSMAPAFGVQEFTVKQGDEVTVTITNIDQIEDVSHGFVVVNHGVSMEISPQQTSSITFVADKPGLHWYYCSWFCHALHMEMVGRMMVEPA 638
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637

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: 7-bladed beta-propeller (245)

Superfamily: Nitrous oxide reductase, N-terminal domain (7)

Family: Nitrous oxide reductase, N-terminal domain (7)

Protein domain: automated matches (5)

Pseudomonas stutzeri [TaxId: 316] (3)

1a	d3sbqa1	A:58-507
1b	d3sbqb1	B:58-507

Fold: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: automated matches (57)

Protein domain: automated matches (57)

Pseudomonas stutzeri [TaxId: 316] (3)

2a	d3sbqa2	A:508-638
2b	d3sbqb2	B:508-638

(no "CATH Domain" information available for 3SBQ)

(no "Pfam Domain" information available for 3SBQ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NOSZ_PSEST | P19573)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0004129	cytochrome-c oxidase activity	Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0050304	nitrous-oxide reductase activity	Catalysis of the reaction: H(2)O + 2 cytochrome c + nitrogen = 2 reduced cytochrome c + nitrous oxide.
	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:0015677	copper ion import	The directed movement of copper ions into a cell or organelle.
	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:1902600	hydrogen ion transmembrane transport	The directed movement of hydrogen ion (proton) across a membrane.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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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	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Ala A:552 - Pro A:553	[ RasMol ]
		Ala B:552 - Pro B:553	[ RasMol ]
		His A:201 - Pro A:202	[ RasMol ]
		His A:428 - Tyr A:429	[ RasMol ]
		His B:201 - Pro B:202	[ RasMol ]
		His B:428 - Tyr B:429	[ RasMol ]
		Pro A:322 - Lys A:323	[ RasMol ]
		Pro B:322 - Lys B:323	[ RasMol ]
		Val A:185 - Pro A:186	[ RasMol ]
		Val A:87 - Pro A:88	[ RasMol ]
		Val B:185 - Pro B:186	[ RasMol ]
		Val B:87 - Pro B:88	[ RasMol ]

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	3sbq
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	NOSZ_PSEST \| P19573
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	1.7.99.6
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	NOSZ_PSEST \| P19573
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UniProtKB/Swiss-Prot
	NOSZ_PSEST \| P19573	:	3sbp 3sbr

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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Gene Ontology (12, 12)

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