2B08 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   REDUCED ACETAMIDE-BOUND M150G NITRITE REDUCTASE FROM ALCALIGENES FAECALIS

Authors :   H. J. Wijma, I. S. Macpherson, O. Farver, E. I. Tocheva, I. Pecht, M. Ph. Verbeet, M. E. P. Murphy, G. W. Canters

Date :   13 Sep 05 (Deposition) - 26 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Axial Methionine, Reorganization Energy, Met62, Allosteric Control, Acetamide, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. J. Wijma, I. Macpherson, O. Farver, E. I. Tocheva, I. Pecht, M. P. Verbeet, M. E. P. Murphy, G. W. Canters
Effect Of The Methionine Ligand On The Reorganization Energy Of The Type-1 Copper Site Of Nitrite Reductase.
J. Am. Chem. Soc. V. 129 519 2007
PubMed-ID: 17227014 | Reference-DOI: 10.1021/JA064763J
(for further references see the PDB file header)

Molecule 1 - COPPER-CONTAINING NITRITE REDUCTASE
	Chains	:	A, B, C
	EC Number	:	1.7.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	NIRK, NIR
	Mutation	:	YES
	Organism Scientific	:	ALCALIGENES FAECALIS
	Organism Taxid	:	511
	Synonym	:	CU-NIR

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 13)

No.	Name	Count	Type	Full Name
1	ACM	4	Ligand/Ion	ACETAMIDE
2	CU1	9	Ligand/Ion	COPPER (I) ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	MET A:62 , HIS A:95 , CYS A:136 , HIS A:145	BINDING SITE FOR RESIDUE CU1 A 1501
02	AC2	SOFTWARE	ASP A:98 , HIS A:100 , HIS A:135 , HIS B:306	BINDING SITE FOR RESIDUE CU1 A 1502
03	AC3	SOFTWARE	MET B:62 , HIS B:95 , CYS B:136 , HIS B:145 , CU1 B:2505	BINDING SITE FOR RESIDUE CU1 B 2501
04	AC4	SOFTWARE	HIS B:100 , HIS B:135 , HIS C:306	BINDING SITE FOR RESIDUE CU1 B 2502
05	AC5	SOFTWARE	MET C:62 , HIS C:95 , CYS C:136 , HIS C:145 , CU1 C:3505	BINDING SITE FOR RESIDUE CU1 C 3501
06	AC6	SOFTWARE	HIS A:306 , HIS C:100 , HIS C:135	BINDING SITE FOR RESIDUE CU1 C 3502
07	AC7	SOFTWARE	HIS B:95 , CYS B:136 , PRO B:138 , HIS B:145 , CU1 B:2501	BINDING SITE FOR RESIDUE CU1 B 2505
08	AC8	SOFTWARE	HIS C:95 , CYS C:136 , PRO C:138 , HIS C:145 , CU1 C:3501	BINDING SITE FOR RESIDUE CU1 C 3505
09	AC9	SOFTWARE	MET A:141 , HIS A:145 , HOH A:1655	BINDING SITE FOR RESIDUE CU1 A 1506
10	BC1	SOFTWARE	GLU A:47 , HIS A:60 , MET A:62 , LEU A:93 , HIS A:95 , PRO A:199 , HOH A:1528	BINDING SITE FOR RESIDUE ACM A 1503
11	BC2	SOFTWARE	MET B:62 , HIS B:95 , TRP B:144 , HIS B:145 , SER B:148	BINDING SITE FOR RESIDUE ACM B 2503
12	BC3	SOFTWARE	HIS C:60 , MET C:62 , LEU C:93 , PRO C:199 , HOH C:3669	BINDING SITE FOR RESIDUE ACM C 3503
13	BC4	SOFTWARE	PRO A:139 , HOH A:1556 , HOH A:1558 , HOH A:1702 , HOH A:1717 , HOH A:1726	BINDING SITE FOR RESIDUE ACM A 1504

(no "SS Bond" information available for 2B08)

Asymmetric/Biological Unit

No.	Residues
1	Pro A:22	-	Pro A:23
2	Val A:68	-	Pro A:69
3	Pro B:22	-	Pro B:23
4	Val B:68	-	Pro B:69
5	Pro C:22	-	Pro C:23
6	Val C:68	-	Pro C:69

(no "SAP(SNP)/Variant" information available for 2B08)

(no "PROSITE Motif" information available for 2B08)

(no "Exon" information available for 2B08)

Asymmetric/Biological 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 NIR_ALCFA | P38501 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:335
                                    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       340       350       360       370     
            NIR_ALCFA    41 TAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 375
               SCOP domains d2b08a1 A:5-161 automated matches                                                                                                                            d2b08a2 A:162-339 automated matches                                                                                                                                                SCOP domains
               CATH domains ------2b08A01 A:11-158 Cupredoxins -  blue copper proteins                                                                                                2b08A02 A:159-325 Cupredoxins -  blue copper proteins                                                                                                                  -------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.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.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b08 A   5 TAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGGNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 339
                                    14        24        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

Chain B from PDB  Type:PROTEIN  Length:336
 aligned with NIR_ALCFA | P38501 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:336
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369      
            NIR_ALCFA    40 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 375
               SCOP domains d2b08b1 B:4-161 automated matches                                                                                                                             d2b08b2 B:162-339 automated matches                                                                                                                                                SCOP domains
               CATH domains -------2b08B01 B:11-158 Cupredoxins -  blue copper proteins                                                                                                2b08B02 B:159-325 Cupredoxins -  blue copper proteins                                                                                                                  -------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh.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.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b08 B   4 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGGNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 339
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333

Chain C from PDB  Type:PROTEIN  Length:336
 aligned with NIR_ALCFA | P38501 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:336
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369      
            NIR_ALCFA    40 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 375
               SCOP domains d2b08c1 C:4-161 automated matches                                                                                                                             d2b08c2 C:162-339 automated matches                                                                                                                                                SCOP domains
               CATH domains -------2b08C01 C:11-158 Cupredoxins -  blue copper proteins                                                                                                2b08C02 C:159-325 Cupredoxins -  blue copper proteins                                                                                                                  -------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhhh..eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b08 C   4 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGGNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 339
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: automated matches (57)

Protein domain: automated matches (57)

Alcaligenes faecalis [TaxId: 511] (9)

1a	d2b08a1	A:5-161
1b	d2b08a2	A:162-339
1c	d2b08b1	B:4-161
1d	d2b08b2	B:162-339
1e	d2b08c1	C:4-161
1f	d2b08c2	C:162-339

Asymmetric/Biological 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 faecalis. Organism_taxid: 511. (13)

1a	2b08A01	A:11-158
1b	2b08B01	B:11-158
1c	2b08C01	C:11-158
1d	2b08A02	A:159-325
1e	2b08B02	B:159-325
1f	2b08C02	C:159-325

(no "Pfam Domain" information available for 2B08)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (NIR_ALCFA | P38501)

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:0019333	denitrification pathway	The reduction of nitrate to dinitrogen by four reactions; each intermediate is transformed to the next lower oxidation state; also part of cellular bioenergetics; the nitrogen compounds can serve as terminal acceptors for electron transport phosphorylation in place of oxygen.
	GO:0042128	nitrate assimilation	The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.
	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.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Pro A:22 - Pro A:23	[ RasMol ]
		Pro B:22 - Pro B:23	[ RasMol ]
		Pro C:22 - Pro C:23	[ RasMol ]
		Val A:68 - Pro A:69	[ RasMol ]
		Val B:68 - Pro B:69	[ RasMol ]
		Val C:68 - Pro C:69	[ RasMol ]

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	2b08
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(no "Related Entries Specified in the PDB File" available for 2B08)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 6)

CATH Domains (1, 6)

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Gene Ontology (9, 9)

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