4CSP - JenaLib

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Title :   STRUCTURE OF THE F306C MUTANT OF NITRITE REDUCTASE FROM ACHROMOBACTER XYLOSOXIDANS

Authors :   N. G. H. Leferink, S. V. Antonyuk, J. A. Houwman, N. S. Scrutton, R. Ready S. S. Hasnain

Date :   09 Mar 14 (Deposition) - 30 Jul 14 (Release) - 12 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Oxidoreductase, Electron Transfer, Microbial Atp-Generating Respiratory Dentrification Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. G. H. Leferink, S. V. Antonyuk, J. A. Houwman, N. S. Scrutton, R. R. Eady, S. S. Hasnain
Impact Of Residues Remote From The Catalytic Centre On Enzyme Catalysis Of Copper Nitrite Reductase.
Nat. Commun. V. 5 4395 2014
PubMed-ID: 25022223 | Reference-DOI: 10.1038/NCOMMS5395

Molecule 1 - DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
	Chains	:	A, F
	EC Number	:	1.7.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET26
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ACHROMOBACTER XYLOSOXIDANS
	Organism Taxid	:	85698
	Strain	:	IW2 IWASAKI

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 13)

No.	Name	Count	Type	Full Name
1	CU	4	Ligand/Ion	COPPER (II) ION
2	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	ZN	7	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	MES	3	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	MES	3	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:89 , CYS A:130 , HIS A:139 , MET A:144	BINDING SITE FOR RESIDUE CU A 501
02	AC2	SOFTWARE	HIS A:94 , HIS A:129 , HIS A:300 , HOH A:1756	BINDING SITE FOR RESIDUE CU A 502
03	AC3	SOFTWARE	HIS A:165 , ASP A:167 , HOH A:1744 , GLU F:195	BINDING SITE FOR RESIDUE ZN A 503
04	AC4	SOFTWARE	CYS A:306	BINDING SITE FOR RESIDUE ZN A 506
05	AC5	SOFTWARE	LEU A:164 , HIS A:165 , THR A:234 , THR A:288 , HOH A:1195	BINDING SITE FOR RESIDUE MES A 510
06	AC6	SOFTWARE	HIS A:313 , HOH A:1212 , HOH A:1710 , HOH A:1755	BINDING SITE FOR RESIDUE ZN A 511
07	AC7	SOFTWARE	HIS F:89 , CYS F:130 , HIS F:139 , MET F:144	BINDING SITE FOR RESIDUE CU F 501
08	AC8	SOFTWARE	HIS F:94 , HIS F:129 , HIS F:300 , HOH F:1757	BINDING SITE FOR RESIDUE CU F 502
09	AC9	SOFTWARE	HIS F:313 , HOH F:1737	BINDING SITE FOR RESIDUE ZN F 503
10	BC1	SOFTWARE	ASP F:4 , HIS F:8 , HOH F:1406 , HOH F:1696	BINDING SITE FOR RESIDUE ZN F 504
11	BC2	SOFTWARE	LEU F:164 , HIS F:165 , THR F:234 , THR F:288 , HOH F:1190	BINDING SITE FOR RESIDUE MES F 505
12	BC3	SOFTWARE	CYS F:306	BINDING SITE FOR RESIDUE ZN F 506
13	BC4	SOFTWARE	GLU A:195 , HIS F:165 , ASP F:167 , HOH F:1740	BINDING SITE FOR RESIDUE ZN F 507

(no "SS Bond" information available for 4CSP)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 4CSP)

(no "PROSITE Motif" information available for 4CSP)

(no "Exon" information available for 4CSP)

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 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4csp A   2 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEACELGAAGHIKVEGKWNDDLMKQIKAPAPIPR 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 F 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 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4csp F   2 DADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEACELGAAGHIKVEGKWNDDLMKQIKAPAPIPR 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 '\|'

(no "SCOP Domain" information available for 4CSP)

(no "CATH Domain" information available for 4CSP)

(no "Pfam Domain" information available for 4CSP)

Asymmetric Unit(hide GO term definitions)

Chain A,F (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.

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

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	4csp
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4csz	STRUCTURE OF F306C MUTANT OF NITRITE REDUCTASE FROM ACHROMOBACTER XYLOSOXIDANS WITH NITRITE BOUND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 13)

Sites (13, 13)

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 (0, 0)

CATH Domains (0, 0)

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