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Title :   LAUE STRUCTURE OF SHEWANELLA ONEIDENSIS CYTOCHROME-C NITRITE REDUCTASE

Authors :   M. Youngblut, E. T. Judd, V. Srajer, B. Sayed, T. Goeltzner, S. Elliott, M. Schmidt, A. Pacheco

Date :   24 Oct 11 (Deposition) - 25 Apr 12 (Release) - 15 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.59

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

Keywords :   Deca-Heme, Electron Transfer, Redox, Cyma, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Youngblut, E. T. Judd, V. Srajer, B. Sayyed, T. Goelzer, S. J. Elliott, M. Schmidt, A. A. Pacheco
Laue Crystal Structure Of Shewanella Oneidensis Cytochrome Nitrite Reductase From A High-Yield Expression System.
J. Biol. Inorg. Chem. V. 17 647 2012
PubMed-ID: 22382353 | Reference-DOI: 10.1007/S00775-012-0885-0

Molecule 1 - CYTOCHROME C-552
	Chains	:	A, B
	EC Number	:	1.7.2.2
	Engineered	:	YES
	Expression System	:	SHEWANELLA
	Expression System Taxid	:	22
	Gene	:	NRFA, SHEWANELLA ONEIDENSIS, SO_3980
	Organism Scientific	:	SHEWANELLA ONEIDENSIS
	Organism Taxid	:	70863
	Synonym	:	AMMONIA-FORMING CYTOCHROME C NITRITE REDUCTASE, CYTOCHROME C NITRITE REDUCTASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 12)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	HEC	10	Ligand/Ion	HEME C

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:86 , ASP A:97 , THR A:101 , ARG A:103 , CYS A:119 , CYS A:122 , LYS A:123 , CYS A:202 , HIS A:203 , TYR A:206 , PHE A:208 , HIS A:257 , HIS A:381 , HEC A:473 , HOH A:488 , HOH A:516 , HOH A:519 , HOH A:531 , HOH A:539	BINDING SITE FOR RESIDUE HEC A 471
02	AC2	SOFTWARE	PHE A:46 , GLN A:49 , GLY A:156 , CYS A:157 , CYS A:160 , HIS A:161 , PRO A:166 , VAL A:276 , MET A:280 , THR A:292 , HIS A:294	BINDING SITE FOR RESIDUE HEC A 472
03	AC3	SOFTWARE	SER A:59 , PRO A:88 , ARG A:89 , HIS A:91 , TYR A:93 , ALA A:94 , ASP A:97 , CYS A:122 , LYS A:123 , ILE A:155 , ASP A:159 , ARG A:172 , VAL A:198 , CYS A:199 , CYS A:202 , HIS A:203 , HIS A:279 , VAL A:296 , GLY A:297 , HEC A:471 , HEC A:474	BINDING SITE FOR RESIDUE HEC A 473
04	AC4	SOFTWARE	PRO A:88 , HIS A:203 , GLU A:259 , TRP A:263 , HIS A:268 , VAL A:273 , SER A:274 , CYS A:275 , CYS A:278 , HIS A:279 , PRO A:299 , LYS A:326 , HIS A:381 , GLY A:382 , ALA A:385 , HIS A:386 , HEC A:473	BINDING SITE FOR RESIDUE HEC A 474
05	AC5	SOFTWARE	ILE A:267 , HIS A:268 , ASN A:271 , VAL A:273 , PRO A:299 , PHE A:300 , THR A:306 , CYS A:307 , CYS A:310 , HIS A:311 , ARG A:325 , HIS B:311 , GLN B:313	BINDING SITE FOR RESIDUE HEC A 475
06	AC6	SOFTWARE	GLU A:205 , TYR A:206 , TYR A:235 , LYS A:254 , GLN A:256	BINDING SITE FOR RESIDUE CA A 476
07	AC7	SOFTWARE	LYS B:86 , PRO B:88 , ASP B:97 , THR B:101 , ARG B:103 , LEU B:115 , CYS B:119 , CYS B:122 , LYS B:123 , CYS B:202 , HIS B:203 , TYR B:206 , PHE B:208 , HIS B:257 , HEC B:473 , HOH B:484 , HOH B:488 , HOH B:499	BINDING SITE FOR RESIDUE HEC B 471
08	AC8	SOFTWARE	PHE B:46 , GLN B:49 , TYR B:50 , GLY B:156 , CYS B:157 , CYS B:160 , HIS B:161 , PRO B:166 , MET B:280 , LYS B:282 , THR B:292 , HIS B:294	BINDING SITE FOR RESIDUE HEC B 472
09	AC9	SOFTWARE	SER B:59 , PRO B:88 , ARG B:89 , GLY B:90 , HIS B:91 , TYR B:93 , ALA B:94 , ASP B:97 , CYS B:122 , ILE B:155 , VAL B:198 , CYS B:199 , GLN B:201 , CYS B:202 , HIS B:203 , HIS B:279 , MET B:280 , VAL B:296 , HEC B:471 , HEC B:474	BINDING SITE FOR RESIDUE HEC B 473
10	BC1	SOFTWARE	HIS B:203 , GLU B:259 , TRP B:263 , HIS B:268 , VAL B:273 , SER B:274 , CYS B:275 , CYS B:278 , HIS B:279 , ASN B:298 , PRO B:299 , LYS B:326 , GLY B:382 , ALA B:385 , HIS B:386 , HEC B:473 , HEC B:475	BINDING SITE FOR RESIDUE HEC B 474
11	BC2	SOFTWARE	HIS A:311 , GLN A:313 , ILE B:267 , HIS B:268 , ASN B:271 , VAL B:273 , PHE B:300 , THR B:306 , CYS B:307 , CYS B:310 , HIS B:311 , ARG B:325 , HEC B:474	BINDING SITE FOR RESIDUE HEC B 475
12	BC3	SOFTWARE	GLU B:205 , TYR B:206 , LYS B:254 , GLN B:256 , HOH B:483	BINDING SITE FOR RESIDUE CA B 476

(no "SS Bond" information available for 3UBR)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:163	-	Gly A:164
2	Gly A:164	-	Ser A:165
3	Met A:224	-	Gly A:225
4	Lys B:163	-	Gly B:164
5	Gly B:164	-	Ser B:165
6	Met B:224	-	Gly B:225

(no "SAP(SNP)/Variant" information available for 3UBR)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTIHEME_CYTC	PS51008	Multiheme cytochrome c family profile.	NRFA_SHEON	148-312	2	A:152-316 B:152-316

(no "Exon" information available for 3UBR)

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:439
 aligned with NRFA_SHEON | Q8EAC7 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:439
                                    37        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         
           NRFA_SHEON    28 SDKTEPRNEVYKDKFKNQYNSWHDTAKSEELVDALEQDPNMVILWAGYAFAKDYKAPRGHMYAVTDVRNTLRTGAPKNAEDGPLPMACWSCKSPDVPRLIEEQGEDGYFKGKWAKGGPEVTNTIGCSDCHEKGSPKLRISRPYVDRALDAIGTPFSKASKQDKESMVCAQCHVEYYFEKKEDKKGFVKFPWDMGVTVDQMEVYYDGIEFSDWTHALSKTPMLKAQHPEYETWKMGIHGKNNVSCVDCHMPKVTSPEGKKFTDHKVGNPFDRFEETCATCHSQTKEFLVGVTNERKAKVKEMKLKAEEQLVKAHFEAAKAWELGATEAEMKPILTDIRHAQWRWDLAIASHGVAAHAPEEALRVLGTSVNKAADARVKLAQLLAKKGLTDPVAIPDISTKAKAQAVLGMDMEKMNAEKEAFKKDMLPKWDAEAKKREATY 466
               SCOP domains d3ubra_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhh........hhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhh..............hhhhhh...hhhhhhhhhhhhhhhh...hhhhh.......hhhhhh..........hhhhhhhhhhh.......hhhhhhhhh........ee.........ee.........hhhhhhhhhh....ee......ee.....hhhhhhh.hhhhhh..hhhhhhh.eee.....eee.....hhhhhh..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------MULTIHEME_CYTC  PDB: A:152-316 UniProt: 148-312                                                                                                                      ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ubr A  32 SDKTEPRNEVYKDKFKNQYNSWHDTAKSEELVDALEQDPNMVILWAGYAFAKDYKAPRGHMYAVTDVRNTLRTGAPKNAEDGPLPMACWSCKSPDVPRLIEEQGEDGYFKGKWAKGGPEVTNTIGCSDCHEKGSPKLRISRPYVDRALDAIGTPFSKASKQDKESMVCAQCHVEYYFEKKEDKKGFVKFPWDMGVTVDQMEVYYDGIEFSDWTHALSKTPMLKAQHPEYETWKMGIHGKNNVSCVDCHMPKVTSPEGKKFTDHKVGNPFDRFEETCATCHSQTKEFLVGVTNERKAKVKEMKLKAEEQLVKAHFEAAKAWELGATEAEMKPILTDIRHAQWRWDLAIASHGVAAHAPEEALRVLGTSVNKAADARVKLAQLLAKKGLTDPVAIPDISTKAKAQAVLGMDMEKMNAEKEAFKKDMLPKWDAEAKKREATY 470
                                    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       341       351       361       371       381       391       401       411       421       431       441       451       461

Chain B from PDB  Type:PROTEIN  Length:439
 aligned with NRFA_SHEON | Q8EAC7 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:439
                                    37        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         
           NRFA_SHEON    28 SDKTEPRNEVYKDKFKNQYNSWHDTAKSEELVDALEQDPNMVILWAGYAFAKDYKAPRGHMYAVTDVRNTLRTGAPKNAEDGPLPMACWSCKSPDVPRLIEEQGEDGYFKGKWAKGGPEVTNTIGCSDCHEKGSPKLRISRPYVDRALDAIGTPFSKASKQDKESMVCAQCHVEYYFEKKEDKKGFVKFPWDMGVTVDQMEVYYDGIEFSDWTHALSKTPMLKAQHPEYETWKMGIHGKNNVSCVDCHMPKVTSPEGKKFTDHKVGNPFDRFEETCATCHSQTKEFLVGVTNERKAKVKEMKLKAEEQLVKAHFEAAKAWELGATEAEMKPILTDIRHAQWRWDLAIASHGVAAHAPEEALRVLGTSVNKAADARVKLAQLLAKKGLTDPVAIPDISTKAKAQAVLGMDMEKMNAEKEAFKKDMLPKWDAEAKKREATY 466
               SCOP domains d3ubrb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhh........hhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh..........hhhhhh....hhhhhhhhhhhhhhhh..............hhhhhh..........hhhhhhhhhhhh......hhhhhhhhhhhh.....ee.........ee.......hhhhhhhhhhhh....ee......ee.....hhhhhhh.hhhhhh..hhhhhhh.eee.....eee.............hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------MULTIHEME_CYTC  PDB: B:152-316 UniProt: 148-312                                                                                                                      ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ubr B  32 SDKTEPRNEVYKDKFKNQYNSWHDTAKSEELVDALEQDPNMVILWAGYAFAKDYKAPRGHMYAVTDVRNTLRTGAPKNAEDGPLPMACWSCKSPDVPRLIEEQGEDGYFKGKWAKGGPEVTNTIGCSDCHEKGSPKLRISRPYVDRALDAIGTPFSKASKQDKESMVCAQCHVEYYFEKKEDKKGFVKFPWDMGVTVDQMEVYYDGIEFSDWTHALSKTPMLKAQHPEYETWKMGIHGKNNVSCVDCHMPKVTSPEGKKFTDHKVGNPFDRFEETCATCHSQTKEFLVGVTNERKAKVKEMKLKAEEQLVKAHFEAAKAWELGATEAEMKPILTDIRHAQWRWDLAIASHGVAAHAPEEALRVLGTSVNKAADARVKLAQLLAKKGLTDPVAIPDISTKAKAQAVLGMDMEKMNAEKEAFKKDMLPKWDAEAKKREATY 470
                                    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       341       351       361       371       381       391       401       411       421       431       441       451       461

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: automated matches (16)

Shewanella oneidensis [TaxId: 70863] (1)

1a	d3ubra_	A:
1b	d3ubrb_	B:

(no "CATH Domain" information available for 3UBR)

(no "Pfam Domain" information available for 3UBR)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NRFA_SHEON | Q8EAC7)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	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:0019645	anaerobic electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors other than oxygen to generate a transmembrane electrochemical gradient.
	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:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	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
		Gly A:164 - Ser A:165	[ RasMol ]
		Gly B:164 - Ser B:165	[ RasMol ]
		Lys A:163 - Gly A:164	[ RasMol ]
		Lys B:163 - Gly B:164	[ RasMol ]
		Met A:224 - Gly A:225	[ RasMol ]
		Met B:224 - Gly B:225	[ RasMol ]

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Ligands, Modified Residues, Ions (2, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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