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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF SPINACH NITRITE REDUCTASE

Authors :   U. Swamy, M. Wang, J. N. Tripathy, S. -K. Kim, M. Hirasawa, D. B. Knaff, J. P. Allen

Date :   03 Aug 05 (Deposition) - 24 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A

Keywords :   X-Ray Crystallography; Heme; Electron Transport, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. Swamy, M. Wang, J. N. Tripathy, S. K. Kim, M. Hirasawa, D. B. Knaff, J. P. Allen
Structure Of Spinach Nitrite Reductase: Implications For Multi-Electron Reactions By The Iron-Sulfur:Siroheme Cofactor
Biochemistry V. 44 16054 2005
PubMed-ID: 16331965 | Reference-DOI: 10.1021/BI050981Y
(for further references see the PDB file header)

Molecule 1 - FERREDOXIN--NITRITE REDUCTASE, CHLOROPLAST
	Chains	:	A
	EC Number	:	1.7.7.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NIR
	Organism Common	:	SPINACH
	Organism Scientific	:	SPINACIA OLERACEA
	Organism Taxid	:	3562
	Other Details	:	SPINACH NITRITE REDUCTASE WAS PRODUCED AS A HIS-TAGGED RECOMBINANT PROTEIN EXPRESSED FROM THE PET30B- NIR PLASMID IN E. COLI. THE E. COLI CELLS WERE CO- TRANSFORMED WITH THE PLASMID PKK233-CYSG THAT CONTAINS THE CYSG GENE ENCODING THE ENZYME THAT CATALYZES THE RATE- LIMITING STEP IN SIROHEME BIOSYNTHESIS.

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER
2	SRM	1	Ligand/Ion	SIROHEME

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:441 , CYS A:447 , ALA A:450 , THR A:480 , GLY A:481 , CYS A:482 , ASN A:484 , CYS A:486	BINDING SITE FOR RESIDUE SF4 A 563
2	AC2	SOFTWARE	ARG A:98 , ARG A:109 , THR A:141 , THR A:142 , ARG A:143 , ASN A:145 , GLN A:147 , ARG A:149 , ARG A:223 , LYS A:224 , ASN A:226 , PHE A:264 , PHE A:265 , SER A:266 , GLN A:306 , ARG A:309 , GLN A:402 , CYS A:441 , THR A:442 , ASN A:484 , CYS A:486 , GLN A:488	BINDING SITE FOR RESIDUE SRM A 564

(no "SS Bond" information available for 2AKJ)

(no "Cis Peptide Bond" information available for 2AKJ)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_NIR_SPIOL_001 *	I	221	V	NIR_SPIOL	---	---	A	I	189	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NIR_SIR	PS00365	Nitrite and sulfite reductases iron-sulfur/siroheme-binding site.	NIR_SPIOL	512-528	1	A:480-496

(no "Exon" information available for 2AKJ)

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:535
 aligned with NIR_SPIOL | P05314 from UniProtKB/Swiss-Prot  Length:594

    Alignment length:535
                                    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       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583     
            NIR_SPIOL    54 RLEPRVEERDGFWVLKEEFRSGINPAEKVKIEKDPMKLFIEDGISDLATLSMEEVDKSKHNKDDIDVRLKWLGLFHRRKHHYGRFMMRLKLPNGVTTSEQTRYLASVIKKYGKDGCADVTTRQNWQIRGVVLPDVPEIIKGLESVGLTSLQSGMDNVRNPVGNPLAGIDPHEIVDTRPFTNLISQFVTANSRGNLSITNLPRKWNPCVIGSHDLYEHPHINDLAYMPATKNGKFGFNLLVGGFFSIKRCEEAIPLDAWVSAEDVVPVCKAMLEAFRDLGFRGNRQKCRMMWLIDELGMEAFRGEVEKRMPEQVLERASSEELVQKDWERREYLGVHPQKQQGLSFVGLHIPVGRLQADEMEELARIADVYGSGELRLTVEQNIIIPNVENSKIDSLLNEPLLKERYSPEPPILMKGLVACTGSQFCGQAIIETKARALKVTEEVQRLVSVTRPVRMHWTGCPNSCGQVQVADIGFMGCMTRDENGKPCEGADVFVGGRIGSDSHLGDIYKKAVPCKDLVPVVAEILINQFGAVPR 588
               SCOP domains d2akja2 A:22-174 Ferredoxin--nitrite reductase, NIR                                                                                                      d2akja4 A:175-345 Ferredoxin--nitrite reductase, NIR                                                                                                                       d2akja1 A:346-430 Ferredoxin--nitrite reductase, NIR                                 d2akja3 A:431-556 Ferredoxin--nitrite reductase, NIR                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..eeee.hhhh...hhhhhhhhhh..hhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhh.eeehhhhhh..eeee..hhh.eeehhhhhhhhhhhhhhhhhh.eee.....eeeeeehhhhhhhhhhhhhh...............................hhhhhhhhhhhhh.....hhhhh.......eee........hhhhh.eeeeeee....eeeeeee..ee....ee..eeeeeeee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..........................eeee.....eeeeee.hhh.eehhhhhhhhhhhhhhhh..eeeee...eeeeeeee..hhhhhh.hhhhhh........hhheeee.hhhhh.......hhhhhhhhhhhhhhhee.....eeeee.......hhhhh.eeeeeeeee.....eeeeeeeee...........eeeeeeee..hhhhhhhhhhhhhh..ee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NIR_SIR          ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2akj A  22 RLEPRVEERDGFWVLKEEFRSGINPAEKVKIEKDPMKLFIEDGISDLATLSMEEVDKSKHNKDDIDVRLKWLGLFHRRKHHYGRFMMRLKLPNGVTTSEQTRYLASVIKKYGKDGCADVTTRQNWQIRGVVLPDVPEIIKGLESVGLTSLQSGMDNVRNPVGNPLAGIDPHEIVDTRPFTNLISQFVTANSRGNLSITNLPRKWNPCVIGSHDLYEHPHINDLAYMPATKNGKFGFNLLVGGFFSIKRCEEAIPLDAWVSAEDVVPVCKAMLEAFRDLGFRGNRQKCRMMWLIDELGMEAFRGEVEKRMPEQVLERASSEELVQKDWERREYLGVHPQKQQGLSFVGLHIPVGRLQADEMEELARIADVYGSGELRLTVEQNIIIPNVENSKIDSLLNEPLLKERYSPEPPILMKGLVACTGSQFCGQAIIETKARALKVTEEVQRLVSVTRPVRMHWTGCPNSCGQVQVADIGFMGCMTRDENGKPCEGADVFVGGRIGSDSHLGDIYKKAVPCKDLVPVVAEILINQFGAVPR 556
                                    31        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

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 '\|'

(no "CATH Domain" information available for 2AKJ)

(no "Pfam Domain" information available for 2AKJ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NIR_SPIOL | P05314)

molecular function
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0048307	ferredoxin-nitrite reductase activity	Catalysis of the reaction: NH3 + 2 H2O + 6 oxidized ferredoxin = nitrite + 6 reduced ferredoxin + 7 H+.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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: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:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

Asymmetric/Biological Unit
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