2XXG - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE N90S MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS

Authors :   M. A. Hough, R. R. Eady, S. S. Hasnain

Date :   10 Nov 10 (Deposition) - 18 May 11 (Release) - 18 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

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

Reference :   M. A. Hough, R. R. Eady, S. S. Hasnain
Identification Of The Proton Channel To The Active Site Type 2 Cu Centre Of Nitrite Reductase: Structural And Enzymatic Properties Of The His254Phe And Asn90Ser Mutants
Biochemistry V. 47 13547 2008
PubMed-ID: 19053252 | Reference-DOI: 10.1021/BI801369Y
(for further references see the PDB file header)

Molecule 1 - DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Mutation	:	YES
	Organism Scientific	:	ACHROMOBACTER XYLOSOXIDANS
	Organism Taxid	:	85698
	Synonym	:	NITRITE REDUCTASE, NIR

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 18)

No.	Name	Count	Type	Full Name
1	CU	4	Ligand/Ion	COPPER (II) ION
2	MES	4	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	PEG	4	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PG4	2	Ligand/Ion	TETRAETHYLENE GLYCOL
5	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 15)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	MES	6	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	PEG	6	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PG4	3	Ligand/Ion	TETRAETHYLENE GLYCOL
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 15)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	MES	6	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	PEG	6	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	PG4	3	Ligand/Ion	TETRAETHYLENE GLYCOL
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:133 , ALA A:296 , PHE A:306 , HIS A:313 , HOH A:2328 , HOH A:2329	BINDING SITE FOR RESIDUE PG4 A 999
02	AC2	SOFTWARE	HIS A:89 , CYS A:130 , HIS A:139 , MET A:144	BINDING SITE FOR RESIDUE CU A1337
03	AC3	SOFTWARE	ASP A:92 , HIS A:94 , HIS A:129 , HIS A:300 , HOH A:2122	BINDING SITE FOR RESIDUE CU A1338
04	AC4	SOFTWARE	HIS A:165 , ASP A:167 , HOH A:2331 , GLU C:195	BINDING SITE FOR RESIDUE ZN A1339
05	AC5	SOFTWARE	MET A:135 , TYR A:197	BINDING SITE FOR RESIDUE PEG A1340
06	AC6	SOFTWARE	ASP A:4 , LEU A:6 , HIS A:8 , HOH A:2332 , HOH A:2333	BINDING SITE FOR RESIDUE ZN A1341
07	AC7	SOFTWARE	ASP A:47 , ASP A:48 , LYS A:49 , PHE A:306 , GLU A:307 , HOH A:2307	BINDING SITE FOR RESIDUE MES A1342
08	AC8	SOFTWARE	PRO A:163 , LEU A:164 , HIS A:165 , THR A:234 , THR A:288 , HOH A:2337	BINDING SITE FOR RESIDUE MES A1343
09	AC9	SOFTWARE	ASP A:121 , ARG A:122 , ARG A:270 , LYS A:290 , HOH A:2336 , HOH A:2339 , HOH A:2340	BINDING SITE FOR RESIDUE PEG A1344
10	BC1	SOFTWARE	VAL C:294 , ALA C:296 , PHE C:306 , HIS C:313 , HOH C:2302	BINDING SITE FOR RESIDUE PG4 C 999
11	BC2	SOFTWARE	ARG C:244 , ASP C:245 , ARG C:247 , ASN C:301 , GLU C:304 , HOH C:2304 , HOH C:2305	BINDING SITE FOR RESIDUE PEG C1337
12	BC3	SOFTWARE	HIS C:89 , CYS C:130 , HIS C:139 , MET C:144	BINDING SITE FOR RESIDUE CU C1338
13	BC4	SOFTWARE	ASP C:92 , HIS C:94 , HIS C:129 , HIS C:300 , HOH C:2111	BINDING SITE FOR RESIDUE CU C1339
14	BC5	SOFTWARE	GLU A:195 , HIS C:165 , ASP C:167 , HOH C:2306	BINDING SITE FOR RESIDUE ZN C1340
15	BC6	SOFTWARE	MET C:135 , ALA C:194	BINDING SITE FOR RESIDUE PEG C1341
16	BC7	SOFTWARE	ASP C:4 , HIS C:8 , HOH C:2307	BINDING SITE FOR RESIDUE ZN C1342
17	BC8	SOFTWARE	ASP C:47 , ASP C:48 , LYS C:49 , PHE C:306 , GLU C:307 , HOH C:2308	BINDING SITE FOR RESIDUE MES C1343
18	BC9	SOFTWARE	LEU C:164 , HIS C:165 , THR C:234 , THR C:288 , HOH C:2245 , HOH C:2309	BINDING SITE FOR RESIDUE MES C1344

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

Asymmetric Unit

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

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

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

(no "Exon" information available for 2XXG)

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: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 d2xxga1 A:2-159 automated matches                                                                                                                             d2xxga2 A:160-336 automated matches                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eee....eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xxg A   2 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHSVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIPR 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 C 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 d2xxgc1 C:2-159 automated matches                                                                                                                             d2xxgc2 C:160-336 automated matches                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------Cu-oxidase_3-2xxgC03 C:38-155                                                                                         ------------Cu-oxidase-2xxgC01 C:168-320                                                                                                                             ---------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------Cu-oxidase_3-2xxgC04 C:38-155                                                                                         ------------Cu-oxidase-2xxgC02 C:168-320                                                                                                                             ---------------- Pfam domains (2)
         Sec.struct. author hhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eee....eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xxg C   2 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHSVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIPR 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(

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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: automated matches (10)

Achromobacter xylosoxidans [TaxId: 85698] (8)

1a	d2xxga1	A:2-159
1b	d2xxga2	A:160-336
1c	d2xxgc1	C:2-159
1d	d2xxgc2	C:160-336

(no "CATH Domain" information available for 2XXG, only for superseded entry 2JL0 replaced by 2XXG)

Asymmetric Unit(hide GO term definitions)

Chain A,C (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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	Cis Peptide Bonds
		Met A:62 - Pro A:63	[ RasMol ]
		Met C:62 - Pro C:63	[ RasMol ]
		Pro A:16 - Pro A:17	[ RasMol ]
		Pro C:16 - Pro C:17	[ RasMol ]

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Access by PDB/NDB ID
	2xxg
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	O68601_ALCXX \| O68601
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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	M144L MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
2bp8	M144Q STRUCTURE OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
2jfc	M144L MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS IN SPACE GROUP P212121
2jl3	CRYSTAL STRUCTURE OF THE CU METALLATED H254F MUTANT OF ALCALIGENES XYLOSOXIDANS CU NITRITE REDUCTASE
2vm3	STRUCTURE OF ALCALIGENES XYLOSOXIDANS IN SPACE GROUP R3 - 1 OF 2
2vm4	STRUCTURE OF ALCALIGENES XYLOSOXIDANS NITRITE REDUCTASE IN SPACE GROUP R3 - 2 OF 2
2vmj	TYPE 1 COPPER-BINDING LOOP OF NITRITE REDUCTASE MUTANT: 130-CAPEGMVPWHVVSGM-144 TO 130-CTPHPFM-136
2vn3	NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
2vw4	NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS - 2 OF 3
2vw6	NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS - 3 OF 3
2vw7	NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS - 1 OF 3
2xwz	STRUCTURE OF THE RECOMBINANT NATIVE NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS COMPLEXED WITH NITRITE
2xx0	STRUCTURE OF THE N90S-H254F MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
2xx1	STRUCTURE OF THE N90S MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS COMPLEXED WITH NITRITE
2xxf	CU METALLATED H254F MUTANT OF NITRITE REDUCTASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 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 (0, 0 ; only for superseded entry 2JL0: 1,4)

Pfam Domains (2, 4)

Gene Ontology (6, 6)

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