2PPA - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   ANAEROBICALLY MANIPULATED WILD TYPE OXIDIZED AFNIR BOUND TO NITROUS OXIDE

Authors :   E. I. Tocheva, M. E. P. Murphy

Date :   28 Apr 07 (Deposition) - 01 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.69

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

Keywords :   Nitrite Reductase, Denitrification, Nitrous Oxide, Bacteria, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. I. Tocheva, L. D. Eltis, M. E. Murphy
Conserved Active Site Residues Limit Inhibition Of A Copper-Containing Nitrite Reductase By Small Molecules.
Biochemistry V. 47 4452 2008
PubMed-ID: 18358002 | Reference-DOI: 10.1021/BI7020537

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
	Organism Scientific	:	ALCALIGENES FAECALIS
	Organism Taxid	:	511
	Strain	:	S-6
	Synonym	:	CU-NIR

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 19)

No.	Name	Count	Type	Full Name
1	ACT	10	Ligand/Ion	ACETATE ION
3	CU	3	Ligand/Ion	COPPER (II) ION
2	CU1	3	Ligand/Ion	COPPER (I) ION
4	N2O	2	Ligand/Ion	NITROUS OXIDE
5	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:95 , CYS A:136 , HIS A:145 , MET A:150	BINDING SITE FOR RESIDUE CU1 A 501
02	AC2	SOFTWARE	HIS A:100 , HIS A:135 , HIS B:306	BINDING SITE FOR RESIDUE CU A 502
03	AC3	SOFTWARE	HIS B:95 , CYS B:136 , HIS B:145 , MET B:150	BINDING SITE FOR RESIDUE CU1 B 501
04	AC4	SOFTWARE	HIS B:100 , HIS B:135 , HIS C:306	BINDING SITE FOR RESIDUE CU B 502
05	AC5	SOFTWARE	HIS C:95 , CYS C:136 , HIS C:145 , MET C:150	BINDING SITE FOR RESIDUE CU1 C 501
06	AC6	SOFTWARE	HIS A:306 , HIS C:100 , HIS C:135	BINDING SITE FOR RESIDUE CU C 502
07	AC7	SOFTWARE	ILE A:257 , HIS A:306 , LEU A:308 , ASP C:98 , HIS C:100 , HIS C:135 , ALA C:137 , HOH C:1593	BINDING SITE FOR RESIDUE ACT C 503
08	AC8	SOFTWARE	ALA A:302 , HOH C:1597	BINDING SITE FOR RESIDUE ACT C 1502
09	AC9	SOFTWARE	GLY B:229 , ILE B:300 , HIS B:319 , HOH B:1722	BINDING SITE FOR RESIDUE ACT B 1503
10	BC1	SOFTWARE	GLU A:113 , HOH A:1549 , ASP B:173 , GLY B:238 , GLU B:239 , LYS B:240 , HOH B:1553	BINDING SITE FOR RESIDUE ACT B 1504
11	BC2	SOFTWARE	GLY B:140 , MET B:141 , PRO B:143 , TRP B:144 , GLU C:313	BINDING SITE FOR RESIDUE ACT B 1505
12	BC3	SOFTWARE	HOH A:1635 , PHE B:282 , PHE C:282 , HOH C:1623 , HOH C:1643 , HOH C:1665 , HOH C:1728	BINDING SITE FOR RESIDUE ACT C 1506
13	BC4	SOFTWARE	HIS C:60 , TYR C:184 , THR C:206 , HOH C:1547 , HOH C:1601	BINDING SITE FOR RESIDUE ACT C 1507
14	BC5	SOFTWARE	GLU A:313 , GLY C:140 , MET C:141 , PRO C:143 , TRP C:144 , MET C:210	BINDING SITE FOR RESIDUE ACT C 1508
15	BC6	SOFTWARE	GLY C:229 , ILE C:300 , HIS C:319 , LYS C:321	BINDING SITE FOR RESIDUE ACT C 1509
16	BC7	SOFTWARE	GLY A:140 , MET A:141 , PRO A:143 , TRP A:144 , TYR A:203 , MET A:210 , GLU B:313 , GLU B:325	BINDING SITE FOR RESIDUE ACT A 1510
17	BC8	SOFTWARE	HIS A:100 , HIS A:135 , HOH A:1601 , ILE B:257 , HIS B:306 , LEU B:308	BINDING SITE FOR RESIDUE N2O A 503
18	BC9	SOFTWARE	HIS B:100 , HIS B:135 , HOH B:1556 , ILE C:257 , HIS C:306 , LEU C:308	BINDING SITE FOR RESIDUE N2O B 503
19	CC1	SOFTWARE	THR A:212 , LEU A:213 , THR A:214 , HOH A:1687 , HOH A:1704 , HOH A:1708 , THR B:212 , LEU B:213 , THR B:214 , THR C:212 , LEU C:213 , THR C:214	BINDING SITE FOR RESIDUE TRS A 1501

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

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 2PPA)

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

(no "Exon" information available for 2PPA)

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: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 d2ppaa1 A:4-166 Nitrite reductase, NIR                                                                                                                             d2ppaa2 A:167-339 Nitrite reductase, NIR                                                                                                                                      SCOP domains
               CATH domains -------2ppaA01 A:11-158 Cupredoxins -  blue copper proteins                                                                                                2ppaA02 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.....hhhhhhh...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
                 2ppa A   4 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 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 B from PDB  Type:PROTEIN  Length:337
 aligned with NIR_ALCFA | P38501 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:337
                                    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 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSGT 376
               SCOP domains d2ppab1 B:4-166 Nitrite reductase, NIR                                                                                                                             d2ppab2 B:167-340 Nitrite reductase, NIR                                                                                                                                       SCOP domains
               CATH domains -------2ppaB01 B:11-158 Cupredoxins -  blue copper proteins                                                                                                2ppaB02 B:159-325 Cupredoxins -  blue copper proteins                                                                                                                  --------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhh...eeeeeee................eeeeeeeeee..............hhhhhhhhhhhhhhh....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ppa B   4 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSGT 340
                                    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 d2ppac1 C:4-166 Nitrite reductase, NIR                                                                                                                             d2ppac2 C:167-339 Nitrite reductase, NIR                                                                                                                                      SCOP domains
               CATH domains -------2ppaC01 C:11-158 Cupredoxins -  blue copper proteins                                                                                                2ppaC02 C:159-325 Cupredoxins -  blue copper proteins                                                                                                                  -------------- CATH domains
           Pfam domains (1) ----------------------------------------Cu-oxidase_3-2ppaC04 C:44-161                                                                                         ------------Cu-oxidase-2ppaC01 C:174-326                                                                                                                             ------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------Cu-oxidase_3-2ppaC05 C:44-161                                                                                         ------------Cu-oxidase-2ppaC02 C:174-326                                                                                                                             ------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------Cu-oxidase_3-2ppaC06 C:44-161                                                                                         ------------Cu-oxidase-2ppaC03 C:174-326                                                                                                                             ------------- Pfam domains (3)
         Sec.struct. author .hhhhhhh..eee.....................eeeeeeeeeeeeee......eeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhh...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
                 2ppa C   4 ATAAEIAALPRQKVELVDPPFVHAHSQVAEGGPKVVEFTMVIEEKKIVIDDAGTEVHAMAFNGTVPGPLMVVHQDDYLELTLINPETNTLMHNIDFHAATGALGGGGLTEINPGEKTILRFKATKPGVFVYHCAPPGMVPWHVVSGMNGAIMVLPREGLHDGKGKALTYDKIYYVGEQDFYVPRDENGKYKKYEAPGDAYEDTVKVMRTLTPTHVVFNGAVGALTGDKAMTAAVGEKVLIVHSQANRDTRPHLIGGHGDYVWATGKFNTPPDVDQETWFIPGGAAGAAFYTFQQPGIYAYVNHNLIEAFELGAAAHFKVTGEWNDDLMTSVLAPSG 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: Multidomain cupredoxins (146)

Protein domain: Nitrite reductase, NIR (79)

Alcaligenes faecalis, strain s-6 [TaxId: 511] (31)

1a	d2ppaa1	A:4-166
1b	d2ppaa2	A:167-339
1c	d2ppab1	B:4-166
1d	d2ppab2	B:167-340
1e	d2ppac1	C:4-166
1f	d2ppac2	C:167-339

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. Strain: s-6. (24)

1a	2ppaA01	A:11-158
1b	2ppaB01	B:11-158
1c	2ppaC01	C:11-158
1d	2ppaA02	A:159-325
1e	2ppaB02	B:159-325
1f	2ppaC02	C:159-325

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Cu-oxidase (74)

Alcaligenes faecalis (18)

1a	Cu-oxidase-2ppaC01	C:174-326
1b	Cu-oxidase-2ppaC02	C:174-326
1c	Cu-oxidase-2ppaC03	C:174-326

Family: Cu-oxidase_3 (79)

Alcaligenes faecalis (18)

2a	Cu-oxidase_3-2ppaC04	C:44-161
2b	Cu-oxidase_3-2ppaC05	C:44-161
2c	Cu-oxidase_3-2ppaC06	C:44-161

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
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		Pro C:22 - Pro C:23	[ RasMol ]
		Val A:68 - Pro A:69	[ RasMol ]
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		Val C:68 - Pro C:69	[ RasMol ]

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	2ppa
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	1.7.2.1
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1sjm	OXIDIZED WILD TYPE AFNIR-NITRITE
1snr	REDUCED WILD TYPE AFNIR-NO

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 19)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 6)

CATH Domains (1, 6)

Pfam Domains (2, 6)

Gene Ontology (9, 9)

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Related Entries Specified in the PDB File