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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CYTOCHROME C NITRITE REDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774: THE RELEVANCE OF THE TWO CALCIUM SITES IN THE STRUCTURE OF THE CATALYTIC SUBUNIT (NRFA).

Authors :   C. A. Cunha, S. Macieira, J. M. Dias, G. Almeida, L. L. Goncalves, C. Costa, J. Lampreia, R. Huber, J. J. G. Moura, I. Moura, M. J. Romao

Date :   14 Jan 03 (Deposition) - 08 May 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Reductase, Cytochrome C, Nitrite Reductase, Nitrogen Cycle, Respiratory Nitrite Ammonification (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. A. Cunha, S. Macieira, J. M. Dias, G. Almeida, L. L. Goncalves, C. Costa, J. Lampreia, R. Huber, J. J. G. Moura, I. Moura, M. J. Romao
Cytochrome C Nitrite Reductase From Desulfovibrio Desulfuricans Atcc 27774. The Relevance Of The Two Calcium Sites In The Structure Of The Catalytic Subunit (Nrfa)
J. Biol. Chem. V. 278 17455 2003
PubMed-ID: 12618432 | Reference-DOI: 10.1074/JBC.M211777200

Molecule 1 - CYTOCHROME C NITRITE REDUCTASE
	Atcc	:	27774
	Chains	:	A, B
	EC Number	:	1.7.2.2
	Organism Scientific	:	DESULFOVIBRIO DESULFURICANS
	Organism Taxid	:	876

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 20)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	CL	4	Ligand/Ion	CHLORIDE ION
3	HEM	10	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:236 , TYR A:237 , LYS A:296 , GLN A:298 , HOH A:2133 , HOH A:2134	BINDING SITE FOR RESIDUE CA A1525
02	AC2	SOFTWARE	GLY A:75 , GLU A:114 , THR A:115 , HEM A:1522 , HEM A:1523	BINDING SITE FOR RESIDUE CA A1526
03	AC3	SOFTWARE	PRO A:107 , PHE A:108 , ARG A:130	BINDING SITE FOR RESIDUE CL A1527
04	AC4	SOFTWARE	HIS A:94 , HIS A:399 , ASP A:462 , CL A:1530 , CL A:1531	BINDING SITE FOR RESIDUE ZN A1528
05	AC5	SOFTWARE	HIS A:94 , HIS A:399 , ASP A:462 , CL A:1530 , CL A:1531	BINDING SITE FOR RESIDUE ZN A1529
06	AC6	SOFTWARE	LYS A:93 , HIS A:94 , HIS A:399 , ASP A:462 , ZN A:1528 , ZN A:1529 , HOH A:2037	BINDING SITE FOR RESIDUE CL A1530
07	AC7	SOFTWARE	LYS A:93 , HIS A:94 , HIS A:399 , ASP A:462 , ZN A:1528 , ZN A:1529 , HOH A:2037	BINDING SITE FOR RESIDUE CL A1531
08	AC8	SOFTWARE	GLU B:236 , TYR B:237 , LYS B:296 , GLN B:298 , HOH B:2138 , HOH B:2140	BINDING SITE FOR RESIDUE CA B1525
09	AC9	SOFTWARE	GLY B:75 , GLU B:114 , THR B:115 , HEM B:1522 , HEM B:1523	BINDING SITE FOR RESIDUE CA B1526
10	BC1	SOFTWARE	PRO B:107 , PHE B:108 , ARG B:130	BINDING SITE FOR RESIDUE CL B1527
11	BC2	SOFTWARE	TYR A:112 , ASN A:113 , THR A:115 , PHE A:125 , ILE A:128 , ARG A:130 , CYS A:146 , CYS A:149 , LYS A:150 , CYS A:233 , HIS A:234 , TYR A:237 , HIS A:299 , ASN A:429 , HEM A:1522 , HOH A:2051 , HOH A:2061 , HOH A:2069 , HOH A:2141 , HOH A:2238 , HOH A:2239 , HOH A:2240	BINDING SITE FOR RESIDUE HEM A1520
12	BC3	SOFTWARE	PHE A:54 , GLN A:57 , GLY A:187 , CYS A:188 , CYS A:191 , HIS A:192 , MET A:197 , ARG A:222 , ARG A:226 , MET A:322 , ILE A:332 , SER A:333 , HIS A:335 , MET A:337 , HEM A:1522	BINDING SITE FOR RESIDUE HEM A1521
13	BC4	SOFTWARE	GLY A:75 , SER A:76 , THR A:115 , ARG A:116 , HIS A:118 , TYR A:120 , ALA A:121 , ASP A:124 , CYS A:149 , LYS A:150 , ILE A:186 , TYR A:202 , VAL A:229 , CYS A:230 , CYS A:233 , HIS A:234 , HIS A:321 , MET A:337 , THR A:338 , HEM A:1520 , HEM A:1521 , HEM A:1523 , CA A:1526 , HOH A:2008	BINDING SITE FOR RESIDUE HEM A1522
14	BC5	SOFTWARE	THR A:71 , LYS A:74 , GLY A:75 , GLU A:114 , THR A:115 , HIS A:234 , GLU A:301 , PHE A:305 , HIS A:310 , SER A:316 , CYS A:317 , CYS A:320 , HIS A:321 , SER A:339 , MET A:341 , GLN A:369 , ASN A:429 , PHE A:433 , HIS A:434 , HEM A:1522 , CA A:1526 , HOH A:2053 , HOH A:2168 , HOH A:2241	BINDING SITE FOR RESIDUE HEM A1523
15	BC6	SOFTWARE	HIS A:310 , ASP A:319 , CYS A:320 , ALA A:348 , CYS A:349 , GLN A:351 , CYS A:352 , HIS A:353 , ARG A:364 , VAL A:365 , HOH A:2167 , HOH A:2242 , HOH A:2243 , HOH A:2244 , HIS B:353 , LYS B:356 , HOH B:2175	BINDING SITE FOR RESIDUE HEM A1524
16	BC7	SOFTWARE	TYR B:112 , ASN B:113 , THR B:115 , PHE B:125 , ILE B:128 , ARG B:130 , CYS B:146 , CYS B:149 , LYS B:150 , CYS B:233 , HIS B:234 , TYR B:237 , HIS B:299 , ASN B:429 , HEM B:1522 , HOH B:2054 , HOH B:2065 , HOH B:2074 , HOH B:2147 , HOH B:2248 , HOH B:2249 , HOH B:2250	BINDING SITE FOR RESIDUE HEM B1520
17	BC8	SOFTWARE	PHE B:54 , GLN B:57 , GLY B:187 , CYS B:188 , CYS B:191 , HIS B:192 , MET B:197 , ARG B:222 , ARG B:226 , MET B:322 , SER B:333 , HIS B:335 , MET B:337 , HEM B:1522 , HOH B:2251	BINDING SITE FOR RESIDUE HEM B1521
18	BC9	SOFTWARE	GLY B:75 , SER B:76 , THR B:115 , ARG B:116 , HIS B:118 , TYR B:120 , ALA B:121 , ASP B:124 , CYS B:149 , ILE B:186 , TYR B:202 , VAL B:229 , CYS B:230 , CYS B:233 , HIS B:234 , HIS B:321 , MET B:337 , THR B:338 , HEM B:1520 , HEM B:1521 , HEM B:1523 , CA B:1526 , HOH B:2014	BINDING SITE FOR RESIDUE HEM B1522
19	CC1	SOFTWARE	THR B:71 , LYS B:74 , GLY B:75 , GLU B:114 , THR B:115 , HIS B:234 , GLU B:301 , PHE B:305 , HIS B:310 , SER B:316 , CYS B:317 , CYS B:320 , HIS B:321 , SER B:339 , MET B:341 , GLN B:369 , ASN B:429 , PHE B:433 , HIS B:434 , HEM B:1522 , CA B:1526 , HOH B:2056 , HOH B:2179 , HOH B:2252	BINDING SITE FOR RESIDUE HEM B1523
20	CC2	SOFTWARE	HIS A:353 , LYS A:356 , HOH A:2165 , HIS B:310 , ASP B:319 , ALA B:348 , CYS B:349 , CYS B:352 , HIS B:353 , ARG B:364 , VAL B:365 , HOH B:2178 , HOH B:2253 , HOH B:2254 , HOH B:2255	BINDING SITE FOR RESIDUE HEM B1524

(no "SS Bond" information available for 1OAH)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:88	-	Pro A:89
2	Leu B:88	-	Pro B:89

(no "SAP(SNP)/Variant" information available for 1OAH)

(no "PROSITE Motif" information available for 1OAH)

(no "Exon" information available for 1OAH)

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:475
 aligned with Q8VNU2_DESDE | Q8VNU2 from UniProtKB/TrEMBL  Length:514

    Alignment length:482
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      514     
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507      |  -  
         Q8VNU2_DESDE    38 TGIAETETKMSAFKGQFPQQYASYMKNNEDRIMTDYKGSVPYHKNDNVNPLPKGFKHAQPYLKNLWLGYPFMYEYNETRGHTYAIDDFLNIDRINRFAADGKGNLPATCWNCKTPKMMEWVSQYGDKFWSMDVNEFRAKDKINAHDETIGCANCHDPATMELRLYSEPLKDWLKRSGKDWQKMSRNEKRTLVCAQCHVEYYFTHKDNGPAAKPVFPWDNGFNPEDMYQYYKGHGAKGPDGKPGPFVDWVHAASKVPMIKMQHPEYETFQDGPHGAAGVSCADCHMQYVREDGKKISSHWMTSPMKDPEMRACRQCHADKTGEYLRQRVLYTQQKTFDQLLKAQEMSVKAHEAVRLANAYEGHRAANYEALMAEAREMVRKGQLFWDYVSAENSVGFHNPAKALDTLMTSMECSQKAVDLATEATDFGIAPALAGDIKKLVPPILTLSRKLQQDPEFLKQNPWTRLLPALPKAEQVWE-----   -
               SCOP domains d1oaha_ A: Cytochrome c nitrite reductase                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1oahA02 A:339-480 Butyryl-CoA Dehydrogenase, subunit A, domain 3                                                                              --------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh..hhhhhhhhhhhhh...............................hhhhhh..hhhhh......hhhhhhhhhhhh...............hhhhh....hhhhhhhhhhhhh....hhhhh............hhhhh...........hhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....ee..........ee.......hhhhhhhhh..eeee.....eee...ee......ee.....hhhhhhh...hhhhh.hhhhhhh..-------.......hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.hhhhhh........hhhhhhhhhh...hhhhh.........ee..ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oah A  38 TGIAETETKMSAFKGQFPQQYASYMKNNEDRIMTDYKGSVPYHKNDNVNPLPKGFKHAQPYLKNLWLGYPFMYEYNETRGHTYAIDDFLNIDRINRFAADGKGNLPATCWNCKTPKMMEWVSQYGDKFWSMDVNEFRAKDKINAHDETIGCANCHDPATMELRLYSEPLKDWLKRSGKDWQKMSRNEKRTLVCAQCHVEYYFTHKDNGPAAKPVFPWDNGFNPEDMYQYYKGHGAKGPDGKPGPFVDWVHAASKVPMIKMQHPEYETFQDGPHGAAGVSCADCHMQY-------ISSHWMTSPMKDPEMRACRQCHADKTGEYLRQRVLYTQQKTFDQLLKAQEMSVKAHEAVRLANAYEGHRAANYEALMAEAREMVRKGQLFWDYVSAENSVGFHNPAKALDTLMTSMECSQKAVDLATEATDFGIAPALAGDIKKLVPPILTLSRKLQQDPEFLKQNPWTRLLPALPKAEQVWEGQDRA 519
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317      |  -    |  337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517  
                                                                                                                                                                                                                                                                                                                        324     332

Chain B from PDB  Type:PROTEIN  Length:482
 aligned with Q8VNU2_DESDE | Q8VNU2 from UniProtKB/TrEMBL  Length:514

    Alignment length:482
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      514     
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507      |  -  
         Q8VNU2_DESDE    38 TGIAETETKMSAFKGQFPQQYASYMKNNEDRIMTDYKGSVPYHKNDNVNPLPKGFKHAQPYLKNLWLGYPFMYEYNETRGHTYAIDDFLNIDRINRFAADGKGNLPATCWNCKTPKMMEWVSQYGDKFWSMDVNEFRAKDKINAHDETIGCANCHDPATMELRLYSEPLKDWLKRSGKDWQKMSRNEKRTLVCAQCHVEYYFTHKDNGPAAKPVFPWDNGFNPEDMYQYYKGHGAKGPDGKPGPFVDWVHAASKVPMIKMQHPEYETFQDGPHGAAGVSCADCHMQYVREDGKKISSHWMTSPMKDPEMRACRQCHADKTGEYLRQRVLYTQQKTFDQLLKAQEMSVKAHEAVRLANAYEGHRAANYEALMAEAREMVRKGQLFWDYVSAENSVGFHNPAKALDTLMTSMECSQKAVDLATEATDFGIAPALAGDIKKLVPPILTLSRKLQQDPEFLKQNPWTRLLPALPKAEQVWE-----   -
               SCOP domains d1oahb_ B: Cytochrome c nitrite reductase                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1oahB02 B:339-480 Butyryl-CoA Dehydrogenase, subunit A, domain 3                                                                              --------------------------------------- CATH domains
           Pfam domains (1) --------Cytochrom_C552-1oahB01 B:46-498                                                                                                                                                                                                                                                                                                                                                                                                                                      --------------------- Pfam domains (1)
           Pfam domains (2) --------Cytochrom_C552-1oahB02 B:46-498                                                                                                                                                                                                                                                                                                                                                                                                                                      --------------------- Pfam domains (2)
         Sec.struct. author .........hhhhhh.hhhhhhhhhhhhh...............................hhhhhh..hhhhh......hhhhhhhhhhhh...............hhhhh....hhhhhhhhhhhhh....hhhhh............hhhhh...........hhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....ee..........ee.......hhhhhhhhh..eeee.....eee...ee......ee.....hhhhhhh...hhhhh.hhhhhhh.eee....eee.....hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhh........hhhhhhhhhh...hhhhh.........ee..ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oah B  38 TGIAETETKMSAFKGQFPQQYASYMKNNEDRIMTDYKGSVPYHKNDNVNPLPKGFKHAQPYLKNLWLGYPFMYEYNETRGHTYAIDDFLNIDRINRFAADGKGNLPATCWNCKTPKMMEWVSQYGDKFWSMDVNEFRAKDKINAHDETIGCANCHDPATMELRLYSEPLKDWLKRSGKDWQKMSRNEKRTLVCAQCHVEYYFTHKDNGPAAKPVFPWDNGFNPEDMYQYYKGHGAKGPDGKPGPFVDWVHAASKVPMIKMQHPEYETFQDGPHGAAGVSCADCHMQYVREDGKKISSHWMTSPMKDPEMRACRQCHADKTGEYLRQRVLYTQQKTFDQLLKAQEMSVKAHEAVRLANAYEGHRAANYEALMAEAREMVRKGQLFWDYVSAENSVGFHNPAKALDTLMTSMECSQKAVDLATEATDFGIAPALAGDIKKLVPPILTLSRKLQQDPEFLKQNPWTRLLPALPKAEQVWEGQDRA 519
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517

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 alpha proteins (14657)

Fold: Multiheme cytochromes (149)

Superfamily: Multiheme cytochromes (149)

Family: Di-heme elbow motif (53)

Protein domain: Cytochrome c nitrite reductase (7)

Desulfovibrio desulfuricans [TaxId: 876] (1)

1a	d1oaha_	A:
1b	d1oahb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Butyryl-CoA Dehydrogenase, subunit A; domain 3 (76)

Homologous Superfamily: Butyryl-CoA Dehydrogenase, subunit A, domain 3 (37)

Desulfovibrio desulfuricans. Organism_taxid: 876. (1)

1a	1oahA02	A:339-480
1b	1oahB02	B:339-480

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Multiheme_cytos (34)

Family: Cytochrom_C552 (6)

Desulfovibrio desulfuricans (1)

1a	Cytochrom_C552-1oahB01	B:46-498
1b	Cytochrom_C552-1oahB02	B:46-498

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q8VNU2_DESDE | Q8VNU2)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0042279	nitrite reductase (cytochrome, ammonia-forming) activity	Catalysis of the reaction: NH3 + 2 H2O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 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: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
		Leu A:88 - Pro A:89	[ RasMol ]
		Leu B:88 - Pro B:89	[ RasMol ]

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	1oah
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	1.7.2.2
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(no "Entries Sharing at Least One Protein Chain" available for 1OAH)

(no "Related Entries Specified in the PDB File" available for 1OAH)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 20)

Sites (20, 20)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (7, 7)

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