1GS8 - JenaLib

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Title :   CRYSTAL STRUCTURE OF MUTANT D92N ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE

Authors :   M. J. Ellis, M. Prudencio, F. E. Dodd, R. W. Strange, G. Sawers, R. R. Eady, S. S. Hasnain

Date :   02 Jan 02 (Deposition) - 14 Feb 02 (Release) - 15 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Oxidoreductase, Multicopper, Periplasmic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Ellis, M. Prudencio, F. E. Dodd, R. W. Strange, G. Sawers, R. R. Eady, S. S. Hasnain
Biochemical And Crystallographic Studies Of The Met144Ala, Asp92Asn And His254Phe Mutants Of The Nitrite Reductase From Alcaligenes Xylosoxidans Provide Insight Into The Enzyme Mechanism.
J. Mol. Biol. V. 316 51 2002
PubMed-ID: 11829502 | Reference-DOI: 10.1006/JMBI.2001.5304

Molecule 1 - DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
	Chains	:	A
	EC Number	:	1.7.99.3, 1.7.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PENIRD92N
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Mutation	:	YES
	Organism Scientific	:	ALCALIGENES XYLOSOXIDANS
	Organism Taxid	:	85698
	Strain	:	N.C.I.M.B. 11015
	Synonym	:	NITRITE REDUCTASE, NIR

		1
Asymmetric Unit	:	A
Biological Unit 1 (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	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

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

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:89 , CYS A:130 , HIS A:139 , MET A:144	BINDING SITE FOR RESIDUE CU A1337
2	AC2	SOFTWARE	ASN A:92 , HIS A:94 , HIS A:129 , HIS A:300 , HOH A:2090	BINDING SITE FOR RESIDUE CU A1338
3	AC3	SOFTWARE	HIS A:165 , ASP A:167 , HOH A:2251 , HOH A:2252	BINDING SITE FOR RESIDUE ZN A1339
4	AC4	SOFTWARE	HIS A:70 , ASP A:73 , HOH A:2253 , HOH A:2254	BINDING SITE FOR RESIDUE ZN A1340
5	AC5	SOFTWARE	ASP A:4 , HIS A:8	BINDING SITE FOR RESIDUE ZN A1341

(no "SS Bond" information available for 1GS8)

Asymmetric Unit

No.	Residues
1	Pro A:16	-	Pro A:17
2	Met A:62	-	Pro A:63

(no "SAP(SNP)/Variant" information available for 1GS8)

(no "PROSITE Motif" information available for 1GS8)

(no "Exon" information available for 1GS8)

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
	(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:336
 aligned with O68601_ALCXX | O68601 from UniProtKB/TrEMBL  Length:360

    Alignment length:336
                                    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       344       354      
         O68601_ALCXX    25 QDADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIPR 360
               SCOP domains d1gs8a1 A:1-159 Nitrite reductase, NIR                                                                                                                         d1gs8a2 A:160-336 Nitrite reductase, NIR                                                                                                                                          SCOP domains
               CATH domains -1gs8A01 A:2-152 Cupredoxins -  blue copper proteins                                                                                                    1gs8A02 A:153-319 Cupredoxins -  blue copper proteins                                                                                                                  ----------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee................eeeeeeeeee...............hhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eee....eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gs8 A   1 QDADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVNFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIPR 336
                                    10        20        30        40        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

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 xylosoxidans [TaxId: 85698] (23)

1a	d1gs8a1	A:1-159
1b	d1gs8a2	A:160-336

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 xylosoxidans. Organism_taxid: 85698. Strain: n.c.i.m.b. 11015. (3)

1a	1gs8A01	A:2-152
1b	1gs8A02	A:153-319

(no "Pfam Domain" information available for 1GS8)

Asymmetric Unit(hide GO term definitions)

Chain A (O68601_ALCXX | O68601)

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: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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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	Cis Peptide Bonds
		Met A:62 - Pro A:63	[ RasMol ]
		Pro A:16 - Pro A:17	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1gs8
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	1.7.2.1
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	1.7.99.3
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1gs6	CRYSTAL STRUCTURE OF M144A MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1gs7	CRYSTAL STRUCTURE OF H254F MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1hau	X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND IN COPPER FREE FORM AT 1.9 ANGSTROMS RESOLUTION
1haw	X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND IN COPPER FREE FORM AT 1.9 ANGSTROMS RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

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