2BP8 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   M144Q STRUCTURE OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS

Authors :   M. A. Hough, M. J. Ellis, S. Antonyuk, R. W. Strange, G. Sawers, R. R. Eady, S. S. Hasnain

Date :   18 Apr 05 (Deposition) - 26 Jul 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Oxidoreductase, Dentrification, Nitrite Reductase, M168Q, Mutant, Electron Transfer, Nitrate Assimilation, Periplasmic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Hough, M. J. Ellis, S. Antonyuk, R. W. Strange, G. Sawers, R. R. Eady, S. S. Hasnain
High Resolution Structural Studies Of Mutants Provide Insights Into Catalysis And Electron Transfer Processes In Copper Nitrite Reductase
J. Mol. Biol. V. 350 300 2005
PubMed-ID: 15927201 | Reference-DOI: 10.1016/J.JMB.2005.04.006

Molecule 1 - DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	ACHROMOBACTER XYLOSOXIDANS
	Organism Taxid	:	85698
	Synonym	:	NITRITE REDUCTASE, NIR

Molecule 2 - DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	ACHROMOBACTER XYLOSOXIDANS
	Organism Taxid	:	85698
	Synonym	:	NITRITE REDUCTASE, NIR

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 18)

No.	Name	Count	Type	Full Name
1	CU	4	Ligand/Ion	COPPER (II) ION
2	SO4	4	Ligand/Ion	SULFATE ION
3	ZN	10	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	SO4	6	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	SO4	6	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:89 , CYS A:130 , HIS A:139 , GLN A:144	BINDING SITE FOR RESIDUE CU A1337
02	AC2	SOFTWARE	HIS A:94 , HIS A:129 , HIS A:300 , HOH A:2177	BINDING SITE FOR RESIDUE CU A1338
03	AC3	SOFTWARE	HIS A:165 , ASP A:167 , HOH A:2417 , GLU B:195	BINDING SITE FOR RESIDUE ZN A1339
04	AC4	SOFTWARE	HIS A:70 , ASP A:73 , HOH A:2418 , HOH A:2419	BINDING SITE FOR RESIDUE ZN A1340
05	AC5	SOFTWARE	HIS A:313 , SO4 A:1344 , SO4 A:1345 , HOH A:2420	BINDING SITE FOR RESIDUE ZN A1341
06	AC6	SOFTWARE	HIS A:8 , GLU A:34 , HOH A:2421 , HOH A:2422	BINDING SITE FOR RESIDUE ZN A1342
07	AC7	SOFTWARE	ASP A:4 , HIS A:8	BINDING SITE FOR RESIDUE ZN A1343
08	AC8	SOFTWARE	HIS A:313 , ZN A:1341 , SO4 A:1345 , HOH A:2424 , HOH A:2425	BINDING SITE FOR RESIDUE SO4 A1344
09	AC9	SOFTWARE	HIS A:313 , ZN A:1341 , SO4 A:1344 , HOH A:2426 , HOH A:2427 , HOH A:2428 , HOH A:2429	BINDING SITE FOR RESIDUE SO4 A1345
10	BC1	SOFTWARE	HIS B:89 , CYS B:130 , HIS B:139 , GLN B:144	BINDING SITE FOR RESIDUE CU B1337
11	BC2	SOFTWARE	HIS B:94 , HIS B:129 , HIS B:300 , HOH B:2136	BINDING SITE FOR RESIDUE CU B1338
12	BC3	SOFTWARE	HIS B:70 , ASP B:73 , HOH B:2351	BINDING SITE FOR RESIDUE ZN B1339
13	BC4	SOFTWARE	GLU A:195 , HIS B:165 , ASP B:167 , HOH B:2352	BINDING SITE FOR RESIDUE ZN B1340
14	BC5	SOFTWARE	HIS B:313 , SO4 B:1344 , SO4 B:1345 , HOH B:2353	BINDING SITE FOR RESIDUE ZN B1341
15	BC6	SOFTWARE	HIS B:8 , GLU B:34 , HOH B:2354 , HOH B:2355 , HOH B:2356	BINDING SITE FOR RESIDUE ZN B1342
16	BC7	SOFTWARE	ASP B:4 , HIS B:8	BINDING SITE FOR RESIDUE ZN B1343
17	BC8	SOFTWARE	HIS B:313 , ZN B:1341 , SO4 B:1345 , HOH B:2358 , HOH B:2359 , HOH B:2361	BINDING SITE FOR RESIDUE SO4 B1344
18	BC9	SOFTWARE	HIS B:313 , ZN B:1341 , SO4 B:1344 , HOH B:2358 , HOH B:2362 , HOH B:2363	BINDING SITE FOR RESIDUE SO4 B1345

(no "SS Bond" information available for 2BP8)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 2BP8)

(no "PROSITE Motif" information available for 2BP8)

(no "Exon" information available for 2BP8)

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:335
 aligned with O68601_ALCXX | O68601 from UniProtKB/TrEMBL  Length:360

    Alignment length:335
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355     
         O68601_ALCXX    26 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIPR 360
               SCOP domains d2bp8a1 A:2-159 automated matches                                                                                                                             d2bp8a2 A:160-336 automated matches                                                                                                                                               SCOP domains
               CATH domains 2bp8A01 A:2-152 Cupredoxins -  blue copper proteins                                                                                                    2bp8A02 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..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eee....eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bp8 A   2 DADKLPHTKVTLVAPPQVHPHEQASKTGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGQSGTLMVLPRDGLKDPEGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIPR 336
                                    11        21        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

Chain B from PDB  Type:PROTEIN  Length:335
 aligned with O68601_ALCXX | O68601 from UniProtKB/TrEMBL  Length:360

    Alignment length:335
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355     
         O68601_ALCXX    26 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIPR 360
               SCOP domains d2bp8b1 B:2-159 automated matches                                                                                                                             d2bp8b2 B:160-336 automated matches                                                                                                                                               SCOP domains
               CATH domains 2bp8B01 B:2-152 Cupredoxins -  blue copper proteins                                                                                                    2bp8B02 B:153-319 Cupredoxins -  blue copper proteins                                                                                                                  ----------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee................eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eee....eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bp8 B   2 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGQSGTLMVLPRDGLKDPEGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIPR 336
                                    11        21        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

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: automated matches (10)

Achromobacter xylosoxidans [TaxId: 85698] (8)

1a	d2bp8a1	A:2-159
1b	d2bp8a2	A:160-336
1c	d2bp8b1	B:2-159
1d	d2bp8b2	B: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)

Achromobacter xylosoxidans. Organism_taxid: 85698. (12)

1a	2bp8A01	A:2-152
1b	2bp8B01	B:2-152
1c	2bp8A02	A:153-319
1d	2bp8B02	B:153-319

(no "Pfam Domain" information available for 2BP8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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
		CU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2bp8
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1bq5	NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS GIFU 1051
1gs6	CRYSTAL STRUCTURE OF M144A MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1gs7	CRYSTAL STRUCTURE OF H254F MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1gs8	CRYSTAL STRUCTURE OF M144A 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 1.9E RESOLUTION
1haw	X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND IN COPPER FREE FORM AT 1.9E RESOLUTION
1ndt	NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
1oe1	ATOMIC RESOLUTION STRUCTURE OF THE WILDTYPE NATIVE NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
1oe2	ATOMIC RESOLUTION STRUCTURE OF D92E MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1oe3	ATOMIC RESOLUTION STRUCTURE OF 'HALF APO' NIR
1wa0	CRYSTAL STRUCTURE OF W138H MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1wa1	CRYSTAL STRUCTURE OF H313Q MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
1wa2	CRYSTAL STRUCTURE OF H313Q MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE WITH NITRITE BOUND
1wae	CRYSTAL STRUCTURE OF H129V MUTANT OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE
2bo0	CRYSTAL STRUCTURE OF THE C130A MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
2bp0	M168L MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

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Related Entries

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Related Entries Specified in the PDB File