2VW4 - JenaLib

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 :   NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS - 2 OF 3

Authors :   M. J. Ellis, S. G. Buffey, M. A. Hough, S. S. Hasnain

Date :   16 Jun 08 (Deposition) - 09 Sep 08 (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 :   Nitrite Reductase, Denitrification, Microspectrophotometer, Ordered Mechanism, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Ellis, S. G. Buffey, M. A. Hough, S. S. Hasnain
On-Line Optical And X-Ray Spectroscopies With Crystallography: An Integrated Approach For Determining Metalloprotein Structures In Functionally Well Defined States.
J. Synchrotron Radiat. V. 15 433 2008
PubMed-ID: 18728313 | Reference-DOI: 10.1107/S0909049508014945

Molecule 1 - DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
	Chains	:	A, B
	EC Number	:	1.7.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	RESIDUES 25-360
	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, 8)

No.	Name	Count	Type	Full Name
1	CU	4	Ligand/Ion	COPPER (II) ION
2	PG4	2	Ligand/Ion	TETRAETHYLENE GLYCOL
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	PG4	3	Ligand/Ion	TETRAETHYLENE GLYCOL
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	PG4	3	Ligand/Ion	TETRAETHYLENE GLYCOL
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

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 A 501
2	AC2	SOFTWARE	ASP A:92 , HIS A:94 , HIS A:129 , HIS A:300 , HOH A:2135	BINDING SITE FOR RESIDUE CU A 502
3	AC3	SOFTWARE	GLU A:195 , HIS B:165 , ASP B:167	BINDING SITE FOR RESIDUE ZN A 503
4	AC4	SOFTWARE	GLU A:133 , VAL A:294 , ALA A:296 , PHE A:306 , ALA A:311 , HIS A:313	BINDING SITE FOR RESIDUE PG4 A 999
5	AC5	SOFTWARE	HIS B:89 , CYS B:130 , HIS B:139 , MET B:144	BINDING SITE FOR RESIDUE CU B 501
6	AC6	SOFTWARE	ASP B:92 , HIS B:94 , HIS B:129 , HIS B:300 , HOH B:2111	BINDING SITE FOR RESIDUE CU B 502
7	AC7	SOFTWARE	HIS A:165 , ASP A:167 , GLU B:195	BINDING SITE FOR RESIDUE ZN B 503
8	AC8	SOFTWARE	GLU B:133 , VAL B:294 , ALA B:296 , PHE B:306 , ALA B:311 , HIS B:313	BINDING SITE FOR RESIDUE PG4 B 999

(no "SS Bond" information available for 2VW4)

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 2VW4)

(no "PROSITE Motif" information available for 2VW4)

(no "Exon" information available for 2VW4)

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:333
 aligned with O68601_ALCXX | O68601 from UniProtKB/TrEMBL  Length:360

    Alignment length:333
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356   
         O68601_ALCXX    27 ADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIP 359
               SCOP domains d2vw4a1 A:3-159 Nitrite reductase, NIR                                                                                                                       d2vw4a2 A:160-335 Nitrite reductase, NIR                                                                                                                                         SCOP domains
               CATH domains 2vw4A01 A:3-152 Cupredoxins -  blue copper proteins                                                                                                   2vw4A02 A: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....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
                 2vw4 A   3 ADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIP 335
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332

Chain B from PDB  Type:PROTEIN  Length:333
 aligned with O68601_ALCXX | O68601 from UniProtKB/TrEMBL  Length:360

    Alignment length:333
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356   
         O68601_ALCXX    27 ADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIP 359
               SCOP domains d2vw4b1 B:3-159 Nitrite reductase, NIR                                                                                                                       d2vw4b2 B:160-335 Nitrite reductase, NIR                                                                                                                                         SCOP domains
               CATH domains 2vw4B01 B:3-152 Cupredoxins -  blue copper proteins                                                                                                   2vw4B02 B:153-319 Cupredoxins -  blue copper proteins                                                                                                                  ---------------- CATH domains
           Pfam domains (1) -----------------------------------Cu-oxidase_3-2vw4B03 B:38-155                                                                                         ------------Cu-oxidase-2vw4B01 B:168-320                                                                                                                             --------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------Cu-oxidase_3-2vw4B04 B:38-155                                                                                         ------------Cu-oxidase-2vw4B02 B:168-320                                                                                                                             --------------- Pfam domains (2)
         Sec.struct. author .....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
                 2vw4 B   3 ADKLPHTKVTLVAPPQVHPHEQATKSGPKVVEFTMTIEEKKMVIDDKGTTLQAMTFNGSMPGPTLVVHEGDYVQLTLVNPATNAMPHNVDFHGATGALGGAKLTNVNPGEQATLRFKADRSGTFVYHCAPEGMVPWHVVSGMSGTLMVLPRDGLKDPQGKPLHYDRAYTIGEFDLYIPKGPDGKYKDYATLAESYGDTVQVMRTLTPSHIVFNGKVGALTGANALTAKVGETVLLIHSQANRDTRPHLIGGHGDWVWETGKFANPPQRDLETWFIRGGSAGAALYTFKQPGVYAYLNHNLIEAFELGAAGHIKVEGKWNDDLMKQIKAPAPIP 335
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332

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	d2vw4a1	A:3-159
1b	d2vw4a2	A:160-335
1c	d2vw4b1	B:3-159
1d	d2vw4b2	B:160-335

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	2vw4A01	A:3-152
1b	2vw4A02	A:153-319
1c	2vw4B02	B:153-319
1d	2vw4B01	B:3-152

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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PG4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	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
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2vw4
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	O68601_ALCXX \| O68601
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	1.7.2.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	O68601_ALCXX \| O68601
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

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
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
2vw6	NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS - 3 OF 3
2vw7	NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS - 1 OF 3

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

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 (2, 4)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File