1NTD - JenaLib

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Title :   STRUCTURE OF ALCALIGENES FAECALIS NITRITE REDUCTASE MUTANT M150E THAT CONTAINS ZINC

Authors :   M. E. P. Murphy, E. T. Adman, S. Turley

Date :   03 Jul 95 (Deposition) - 08 Nov 96 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Oxidoreductase, Flavoprotein, Fad, Nitrate Assimilation, Oxidoreductase (Nitric Oxide(A)) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Murphy, S. Turley, M. Kukimoto, M. Nishiyama, S. Horinouchi, H. Sasaki, M. Tanokura, E. T. Adman
Structure Of Alcaligenes Faecalis Nitrite Reductase And A Copper Site Mutant, M150E, That Contains Zinc.
Biochemistry V. 34 12107 1995
PubMed-ID: 7547950 | Reference-DOI: 10.1021/BI00038A003
(for further references see the PDB file header)

Molecule 1 - NITRITE REDUCTASE
	Chains	:	A
	EC Number	:	1.7.99.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	NIR
	Expression System Plasmid	:	PNIR601
	Expression System Strain	:	JM105
	Expression System Taxid	:	562
	Gene	:	NIR
	Mutation	:	YES
	Organism Scientific	:	ALCALIGENES FAECALIS
	Organism Taxid	:	511
	Strain	:	STRAIN S-6

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

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

Biological Unit 1 (0, 0)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:95 , CYS A:136 , HIS A:145 , GLU A:150	BINDING SITE FOR RESIDUE CU A 501
2	AC2	SOFTWARE	HIS A:100 , HIS A:135 , HIS A:306 , HOH A:503	BINDING SITE FOR RESIDUE CU A 502
3	CU1	UNKNOWN	HIS A:95 , CYS A:136 , HIS A:145 , GLU A:150	TYPE I SITE
4	CU2	UNKNOWN	HIS A:100 , HIS A:135 , HIS A:306 , HOH A:503	TYPE II SITE SITE CU2 IS BOUND BETWEEN TWO MONOMERS BY HIS 100, HIS 135 ON ONE AND HIS 306 FROM ANOTHER MONOMER ON THE OTHER.

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

Asymmetric Unit

No.	Residues
1	Pro A:22	-	Pro A:23
2	Val A:68	-	Pro A:69

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

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

(no "Exon" information available for 1NTD)

Asymmetric 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
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Chain A from PDB  Type:PROTEIN  Length:336
 aligned with NIR_ALCFA | P38501 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:336
                                    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_ALCFA    41 TAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSGT 376
               SCOP domains d1ntda1 A:5-166 Nitrite reductase, NIR                                                                                                                            d1ntda2 A:167-340 Nitrite reductase, NIR                                                                                                                                       SCOP domains
               CATH domains ----1ntdA01 A:9-158 Cupredoxins -  blue copper proteins                                                                                                   1ntdA02 A:159-325 Cupredoxins -  blue copper proteins                                                                                                                  --------------- CATH domains
               Pfam domains ---------------------------------------Cu-oxidase_3-1ntdA02 A:44-161                                                                                         ------------Cu-oxidase-1ntdA01 A:174-326                                                                                                                             -------------- Pfam domains
         Sec.struct. author .........eee.....................eeeeeeeeeeeeee......eeeeeee.......eeeee...eeeeeeee.................hhhh.........eeeeeeee....eeeeee......hhhhhhh..eeeeeee................eeeeeeeeee...............hhhhhhhhhhhhhh....eeee............eeee...eeeeeeee......eeee.....eee.....................eeeeeeee....eeeeeee..hhhhh....eeeeeee................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ntd A   5 TAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGENGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSGT 340
                                    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

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(

)

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)

Alcaligenes faecalis, strain s-6 [TaxId: 511] (31)

1a	d1ntda1	A:5-166
1b	d1ntda2	A:167-340

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Cupredoxins - blue copper proteins (420)

Alcaligenes faecalis. Organism_taxid: 511. Strain: strain s-6. (1)

1a	1ntdA01	A:9-158
1b	1ntdA02	A:159-325

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Cu-oxidase (74)

Alcaligenes faecalis (18)

Cu-oxidase-1ntdA01

A:174-326

Family: Cu-oxidase_3 (79)

Alcaligenes faecalis (18)

Cu-oxidase_3-1ntdA02

A:44-161

Asymmetric Unit(hide GO term definitions)

Chain A (NIR_ALCFA | P38501)

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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		Val A:68 - Pro A:69	[ RasMol ]

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		Biological Unit 1	[ Jena3D ]

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Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (0, 0)

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