1N70 - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF NITRITE REDUCTASE MUTANT HIS287ALA FROM RHODOBACTER SPHAEROIDES

Authors :   H. Guo, K. Olesen, J. Shapliegh, L. Sjolin

Date :   12 Nov 02 (Deposition) - 28 Sep 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: A  (3x)

Keywords :   Nitrite Reductase, Mutant H287A, Electron Transfer, Nitrite Oxide, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Guo, K. Olesen, J. Shapliegh, L. Sjolin
The Crystal Structure Of Nitrite Reductase Mutant His287Ala From Rhodobacter Sphaeroides To 1. 6 Resolution
To Be Published
PubMed: search

Molecule 1 - COPPER-CONTAINING NITRITE REDUCTASE PRECURSOR
	Chains	:	A
	EC Number	:	1.7.99.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 41-374
	Gene	:	NIRK
	Mutation	:	YES
	Organism Scientific	:	RHODOBACTER SPHAEROIDES
	Organism Taxid	:	1063
	Strain	:	2.4.3
	Synonym	:	CU-NIR

		1
Asymmetric Unit	:	A
Biological Unit 1 (3x)	:	A
Biological Unit 2 (1x)	:	A
Biological Unit 3 (3x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CU	2	Ligand/Ion	COPPER (II) ION
2	MG	3	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:126 , CYS A:167 , HIS A:177 , MET A:182	BINDING SITE FOR RESIDUE CU A 401
2	AC2	SOFTWARE	HIS A:131 , HIS A:166 , HIS A:338 , HOH A:779	BINDING SITE FOR RESIDUE CU A 402
3	AC3	SOFTWARE	ASP A:220 , THR A:224 , HOH A:636 , HOH A:803 , HOH A:804 , HOH A:805	BINDING SITE FOR RESIDUE MG A 501
4	AC4	SOFTWARE	HOH A:806 , HOH A:807 , HOH A:808 , HOH A:809 , HOH A:810 , HOH A:811	BINDING SITE FOR RESIDUE MG A 502
5	AC5	SOFTWARE	HOH A:664 , HOH A:707 , HOH A:746 , HOH A:801 , HOH A:802 , HOH A:840	BINDING SITE FOR RESIDUE MG A 503

(no "SS Bond" information available for 1N70)

Asymmetric Unit

No.	Residues
1	Pro A:54	-	Pro A:55
2	Ile A:99	-	Pro A:100

(no "SAP(SNP)/Variant" information available for 1N70)

(no "PROSITE Motif" information available for 1N70)

(no "Exon" information available for 1N70)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:334
 aligned with NIR_RHOS5 | Q53239 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:334
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370    
            NIR_RHOS5    41 LSNLPRVKHTLVPPPFAHAHEQVAASGPVINEFEMRIIEKEVQLDEDAYLQAMTFDGSIPGPLMIVHEGDYVELTLINPPENTMPHNIDFHAATGALGGGGLTLINPGEKVVLRFKATRAGAFVYHCAPGGPMIPWHVVSGMAGCIMVLPRDGLKDHEGKPVRYDTVYYIGESDHYIPKDEDGTYMRFSDPSEGYEDMVAVMDTLIPSHIVFNGAVGALTGEGALKAKVGDNVLFVHSQPNRDSRPHLIGGHGDLVWETGKFHNAPERDLETWFIRGGSAGAALYKFLQPGVYAYVNHNLIEAVHKGATAHVLVEGEWDNDLMEQVVAPVGLTG 374
               SCOP domains d1n70a1 A:41-193 Nitrite reductase, NIR                                                                                                                  d1n70a2 A:194-371 Nitrite reductase, NIR                                                                                                                                          --- SCOP domains
               CATH domains 1n70A01 A:41-190 Cupredoxins -  blue copper proteins                                                                                                  1n70A02 A:191-374 Cupredoxins -  blue copper proteins                                                                                                                                    CATH domains
               Pfam domains -----------------------------------Cu-oxidase_3-1n70A02 A:76-193                                                                                         ------------Cu-oxidase-1n70A01 A:206-358                                                                                                                             ---------------- Pfam domains
         Sec.struct. author .....eee.....................eeeeeeeeeeeeeeee..eeeeeeee.......eeeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhhh..eeeeeee................eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n70 A  41 LSNLPRVKHTLVPPPFAHAHEQVAASGPVINEFEMRIIEKEVQLDEDAYLQAMTFDGSIPGPLMIVHEGDYVELTLINPPENTMPHNIDFHAATGALGGGGLTLINPGEKVVLRFKATRAGAFVYHCAPGGPMIPWHVVSGMAGCIMVLPRDGLKDHEGKPVRYDTVYYIGESDHYIPKDEDGTYMRFSDPSEGYEDMVAVMDTLIPSHIVFNGAVGALTGEGALKAKVGDNVLFVHSQPNRDSRPALIGGHGDLVWETGKFHNAPERDLETWFIRGGTAGAALYKFLQPGVYAYVNHNLIEAVHKGATAHVLVEGEWDNDLMEQVVAPVGLTG 374
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370

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 Unit

Classes(

)

Folds(

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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)

Rhodobacter sphaeroides [TaxId: 1063] (8)

1a	d1n70a1	A:41-193
1b	d1n70a2	A:194-371

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Cupredoxins - blue copper proteins (420)

Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: 2.4.3. (4)

1a	1n70A01	A:41-190
1b	1n70A02	A:191-374

Asymmetric Unit(hide GO term definitions)

Chain A (NIR_RHOS5 | Q53239)

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).

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