1FGJ - JenaLib

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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 :   X-RAY STRUCTURE OF HYDROXYLAMINE OXIDOREDUCTASE

Authors :   N. Tanaka, N. Igarashi, H. Moriyama

Date :   03 Mar 97 (Deposition) - 04 Mar 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (3x)
Biol. Unit 2: B  (3x)

Keywords :   Oxidoreductase, Nitrification (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Igarashi, H. Moriyama, T. Fujiwara, Y. Fukumori, N. Tanaka
The 2. 8 A Structure Of Hydroxylamine Oxidoreductase From A Nitrifying Chemoautotrophic Bacterium, Nitrosomonas Europaea.
Nat. Struct. Biol. V. 4 276 1997
PubMed-ID: 9095195 | Reference-DOI: 10.1038/NSB0497-276

Molecule 1 - HYDROXYLAMINE OXIDOREDUCTASE
	Atcc	:	19178
	Chains	:	A, B
	EC Number	:	1.7.3.4
	Organism Scientific	:	NITROSOMONAS EUROPAEA
	Organism Taxid	:	915

		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 (2, 16)

No.	Name	Count	Type	Full Name
1	HEC	2	Ligand/Ion	HEME C
2	HEM	14	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (2, 24)

No.	Name	Count	Type	Full Name
1	HEC	3	Ligand/Ion	HEME C
2	HEM	21	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (2, 24)

No.	Name	Count	Type	Full Name
1	HEC	3	Ligand/Ion	HEME C
2	HEM	21	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:57 , TYR A:64 , PRO A:67 , SER A:69 , ALA A:74 , CYS A:79 , CYS A:82 , HIS A:83 , GLU A:86 , CYS A:145 , ILE A:146 , HIS A:149 , HIS A:160 , SER A:365 , GLU A:366 , ARG A:367 , HEM A:548	BINDING SITE FOR RESIDUE HEM A 547
02	AC2	SOFTWARE	TYR A:57 , PRO A:60 , HIS A:83 , TRP A:90 , TRP A:94 , HIS A:99 , VAL A:143 , GLY A:144 , CYS A:145 , CYS A:148 , HIS A:149 , MET A:166 , PRO A:167 , LYS A:238 , ASP A:240 , ARG A:245 , HIS A:246 , PHE A:248 , HIS A:364 , SER A:365 , HEM A:547 , HEM A:549	BINDING SITE FOR RESIDUE HEM A 548
03	AC3	SOFTWARE	THR A:98 , HIS A:99 , LYS A:117 , LYS A:120 , LEU A:121 , VAL A:143 , CYS A:172 , CYS A:175 , HIS A:176 , CYS A:239 , PHE A:248 , ALA A:250 , HEM A:548 , HEM A:551	BINDING SITE FOR RESIDUE HEM A 549
04	AC4	SOFTWARE	TRP A:197 , ARG A:201 , ALA A:210 , ASN A:211 , THR A:214 , GLY A:228 , CYS A:229 , CYS A:232 , HIS A:233 , THR A:261 , CYS A:262 , HIS A:263 , HIS A:268 , ALA A:332 , ASN A:333 , THR A:466 , TYR A:467 , HEM A:552 , HEM A:553	BINDING SITE FOR RESIDUE HEC A 550
05	AC5	SOFTWARE	TYR A:116 , LYS A:117 , CYS A:172 , HIS A:176 , GLU A:179 , HIS A:204 , ASN A:235 , CYS A:239 , CYS A:242 , HIS A:243 , SER A:253 , ARG A:254 , ARG A:295 , LEU A:296 , MET A:315 , HIS A:323 , HEM A:549 , HEM A:552	BINDING SITE FOR RESIDUE HEM A 551
06	AC6	SOFTWARE	PRO A:202 , SER A:203 , HIS A:204 , ASP A:207 , ALA A:210 , MET A:231 , CYS A:232 , HIS A:233 , ASN A:235 , ASN A:241 , CYS A:242 , ALA A:258 , CYS A:259 , CYS A:262 , HIS A:263 , ILE A:325 , THR A:329 , HEC A:550 , HEM A:551 , HEM A:553	BINDING SITE FOR RESIDUE HEM A 552
07	AC7	SOFTWARE	HIS A:263 , ASN A:270 , TYR A:274 , THR A:309 , CYS A:310 , CYS A:313 , HIS A:314 , ARG A:330 , TRP A:331 , TRP A:356 , MET A:376 , HIS A:459 , HEC A:550 , HEM A:552 , HEM A:554	BINDING SITE FOR RESIDUE HEM A 553
08	AC8	SOFTWARE	TRP A:90 , MET A:231 , LYS A:238 , ASP A:240 , THR A:244 , ARG A:245 , HIS A:279 , PHE A:300 , ASN A:306 , ALA A:307 , PRO A:308 , THR A:359 , CYS A:360 , CYS A:363 , HIS A:364 , PHE A:368 , TYR A:372 , VAL A:460 , HEM A:553	BINDING SITE FOR RESIDUE HEM A 554
09	AC9	SOFTWARE	TYR B:57 , TYR B:64 , PRO B:67 , ALA B:74 , ASP B:78 , CYS B:79 , CYS B:82 , HIS B:83 , HIS B:149 , HIS B:160 , SER B:365 , GLU B:366 , ARG B:367 , HEM B:548	BINDING SITE FOR RESIDUE HEM B 547
10	BC1	SOFTWARE	TYR B:57 , HIS B:83 , TRP B:90 , HIS B:99 , VAL B:143 , GLY B:144 , CYS B:145 , CYS B:148 , HIS B:149 , MET B:166 , PRO B:167 , LYS B:238 , ASP B:240 , ARG B:245 , HIS B:246 , PHE B:248 , HIS B:364 , SER B:365 , HEM B:547 , HEM B:549	BINDING SITE FOR RESIDUE HEM B 548
11	BC2	SOFTWARE	THR B:98 , HIS B:99 , LEU B:102 , LYS B:117 , LYS B:120 , LEU B:121 , VAL B:143 , CYS B:172 , CYS B:175 , HIS B:176 , CYS B:239 , PHE B:248 , ALA B:250 , HEM B:548 , HEM B:551	BINDING SITE FOR RESIDUE HEM B 549
12	BC3	SOFTWARE	TRP B:197 , ARG B:201 , ALA B:210 , ASN B:211 , THR B:214 , TRP B:217 , GLY B:228 , CYS B:229 , CYS B:232 , HIS B:233 , THR B:261 , CYS B:262 , HIS B:263 , HIS B:268 , ALA B:332 , ASN B:333 , THR B:466 , TYR B:467 , HEM B:552 , HEM B:553	BINDING SITE FOR RESIDUE HEC B 550
13	BC4	SOFTWARE	TYR B:116 , LYS B:117 , CYS B:172 , HIS B:176 , GLU B:179 , ASN B:235 , CYS B:239 , CYS B:242 , HIS B:243 , SER B:253 , ARG B:254 , ARG B:295 , LEU B:296 , MET B:315 , HIS B:323 , HEM B:549 , HEM B:552	BINDING SITE FOR RESIDUE HEM B 551
14	BC5	SOFTWARE	PRO B:202 , SER B:203 , HIS B:204 , ALA B:210 , CYS B:232 , HIS B:233 , ASN B:235 , ASN B:241 , CYS B:259 , CYS B:262 , HIS B:263 , ALA B:332 , HEC B:550 , HEM B:551 , HEM B:553	BINDING SITE FOR RESIDUE HEM B 552
15	BC6	SOFTWARE	CYS B:259 , HIS B:263 , ASN B:270 , TRP B:271 , TYR B:274 , PRO B:308 , THR B:309 , CYS B:310 , CYS B:313 , HIS B:314 , ARG B:330 , TRP B:331 , TRP B:356 , ALA B:458 , HIS B:459 , HEC B:550 , HEM B:552 , HEM B:554	BINDING SITE FOR RESIDUE HEM B 553
16	BC7	SOFTWARE	LYS B:238 , ASP B:240 , THR B:244 , ARG B:245 , HIS B:279 , LEU B:282 , ASN B:306 , THR B:359 , CYS B:360 , CYS B:363 , HIS B:364 , PHE B:368 , TYR B:372 , HEM B:553	BINDING SITE FOR RESIDUE HEM B 554

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

Asymmetric Unit

No.	Residues
1	Arg A:201	-	Pro A:202
2	Glu A:415	-	Pro A:416
3	Asn A:434	-	Pro A:435
4	Arg B:201	-	Pro B:202
5	Glu B:415	-	Pro B:416
6	Asn B:434	-	Pro B:435

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTIHEME_CYTC	PS51008	Multiheme cytochrome c family profile.	HAO_NITEU	98-393	2	A:74-369 B:74-369

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTIHEME_CYTC	PS51008	Multiheme cytochrome c family profile.	HAO_NITEU	98-393	3	A:74-369 -

Biological Unit 2 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTIHEME_CYTC	PS51008	Multiheme cytochrome c family profile.	HAO_NITEU	98-393	3	- B:74-369

(no "Exon" information available for 1FGJ)

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:499
 aligned with HAO_NITEU | Q50925 from UniProtKB/Swiss-Prot  Length:570

    Alignment length:499
                                    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       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514         
            HAO_NITEU    25 DISTVPDETYDALKLDRGKATPKETYEALVKRYKDPAHGAGKGTMGDYWEPIAISIYMDPNTFYKPPVSPKEVAERKDCVECHSDETPVWVRAWKRSTHANLDKIRNLKSDDPLYYKKGKLEEVENNLRSMGKLGEKETLKEVGCIDCHVDVNKKDKADHTKDIRMPTADTCGTCHLREFAERESERDTMVWPNGQWPAGRPSHALDYTANIETTVWAAMPQREVAEGCTMCHTNQNKCDNCHTRHEFSAAESRKPEACATCHSGVDHNNWEAYTMSKHGKLAEMNRDKWNWEVRLKDAFSKGGQNAPTCAACHMEYEGEYTHNITRKTRWANYPFVPGIAENITSDWSEARLDSWVLTCTQCHSERFARSYLDLMDKGTLEGLAKYQEANAIVHKMYEDGTLTGQKTNRPNPPEPEKPGFGIFTQLFWSKGNNPASLELKVLEMAENNLAKMHVGLAHVNPGGWTYTEGWGPMNRAYVEIQDEYTKMQELSALQARVN 523
               SCOP domains d1fgja_ A: Hydroxylamine oxidoreductase, HAO                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1fgjA01 A:1-240 Hydroxylamine Oxidoreductase; Chain A, domain 1                                                                                                                                                                                 -----------------------------1fgjA02 A:270-499 Hydroxylamine Oxidoreductase; Chain A, domain 2                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh........hhhhhhhhhhhhh.hhh.......hhh....hhhhhh.hhhh.........ee.hhhhhhhhhhh.hhhhhhhh......hhhhh......hhhhhhhhhhhhhhhhhh..............hhhhh........eehhhh.....hhhhhh..hhhhhhhhhhhhh.................hhhhhh..hhhhh...hhhhhhhhhh.................hhhhh.hhhhh.........hhhhhhh.hhhhhhhhh.........hhhh..........hhhhh..........................hhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................hhhh.........hhhhhhhhhhh.hhhhhhhhhh...hhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------MULTIHEME_CYTC  PDB: A:74-369 UniProt: 98-393                                                                                                                                                                                                                                                           ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fgj A   1 DISTVPDETYDALKLDRGKATPKETYEALVKRYKDPAHGAGKGTMGDYWEPIAISIYMDPNTFYKPPVSPKEVAERKDCVECHSDETPVWVRAWKRSTHANLDKIRNLKSDDPLYYKKGKLEEVENNLRSMGKLGEKETLKEVGCIDCHVDVNKKDKADHTKDIRMPTADTCGTCHLREFAERESERDTMVWPNGQWPAGRPSHALDYTANIETTVWATMPQREVAEGCTMCHTNQNKCDNCHTRHEFSAAESRKPEACATCHSGVDHNNWEAYTMSKHGKLAEMNRDKWNWEVRLKDAFSKGGQNAPTCAACHMEYEGEYTHNITRKTRWANYPFVPGIAENITSDWSEARLDSWVLTCTQCHSERFARSYLDLMDKGTLEGLAKYQEANAIVHKMYEDGTLTGQKTNRPNPPEPEKPGFGIFTQLFWSKGNNPASLELKVLEMGENNLAKMHVGLAHVNPGGWTYTEGWGPMNRAYVEIQDEYTKMQELSALQARVN 499
                                    10        20        30        40        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       380       390       400       410       420       430       440       450       460       470       480       490

Chain B from PDB  Type:PROTEIN  Length:499
 aligned with HAO_NITEU | Q50925 from UniProtKB/Swiss-Prot  Length:570

    Alignment length:499
                                    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       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514         
            HAO_NITEU    25 DISTVPDETYDALKLDRGKATPKETYEALVKRYKDPAHGAGKGTMGDYWEPIAISIYMDPNTFYKPPVSPKEVAERKDCVECHSDETPVWVRAWKRSTHANLDKIRNLKSDDPLYYKKGKLEEVENNLRSMGKLGEKETLKEVGCIDCHVDVNKKDKADHTKDIRMPTADTCGTCHLREFAERESERDTMVWPNGQWPAGRPSHALDYTANIETTVWAAMPQREVAEGCTMCHTNQNKCDNCHTRHEFSAAESRKPEACATCHSGVDHNNWEAYTMSKHGKLAEMNRDKWNWEVRLKDAFSKGGQNAPTCAACHMEYEGEYTHNITRKTRWANYPFVPGIAENITSDWSEARLDSWVLTCTQCHSERFARSYLDLMDKGTLEGLAKYQEANAIVHKMYEDGTLTGQKTNRPNPPEPEKPGFGIFTQLFWSKGNNPASLELKVLEMAENNLAKMHVGLAHVNPGGWTYTEGWGPMNRAYVEIQDEYTKMQELSALQARVN 523
               SCOP domains d1fgjb_ B: Hydroxylamine oxidoreductase, HAO                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1fgjB01 B:1-240 Hydroxylamine Oxidoreductase; Chain A, domain 1                                                                                                                                                                                 -----------------------------1fgjB02 B:270-499 Hydroxylamine Oxidoreductase; Chain A, domain 2                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh........hhhhhhhhhhhhh.hhh.....hhhhh....hhhhhh.hhhh.........ee.hhhhhhhhhhh.hhhhhhhh..hhh.hhhhh......hhhhhhhhhhhhhhhhhh..............hhhhh........ee.........hhhhhhh.hhhhhhhhhhhhh.................hhhhhh..hhhhh...hhhhhhhhhh...................hhh.hhhhh.........hhhhhhh.hhhhhhhh.hhh....................hhhhhh........................hhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhh........hhhhhhhhhhh.hhhhhhhhhh...hhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------MULTIHEME_CYTC  PDB: B:74-369 UniProt: 98-393                                                                                                                                                                                                                                                           ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fgj B   1 DISTVPDETYDALKLDRGKATPKETYEALVKRYKDPAHGAGKGTMGDYWEPIAISIYMDPNTFYKPPVSPKEVAERKDCVECHSDETPVWVRAWKRSTHANLDKIRNLKSDDPLYYKKGKLEEVENNLRSMGKLGEKETLKEVGCIDCHVDVNKKDKADHTKDIRMPTADTCGTCHLREFAERESERDTMVWPNGQWPAGRPSHALDYTANIETTVWATMPQREVAEGCTMCHTNQNKCDNCHTRHEFSAAESRKPEACATCHSGVDHNNWEAYTMSKHGKLAEMNRDKWNWEVRLKDAFSKGGQNAPTCAACHMEYEGEYTHNITRKTRWANYPFVPGIAENITSDWSEARLDSWVLTCTQCHSERFARSYLDLMDKGTLEGLAKYQEANAIVHKMYEDGTLTGQKTNRPNPPEPEKPGFGIFTQLFWSKGNNPASLELKVLEMGENNLAKMHVGLAHVNPGGWTYTEGWGPMNRAYVEIQDEYTKMQELSALQARVN 499
                                    10        20        30        40        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       380       390       400       410       420       430       440       450       460       470       480       490

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 alpha proteins (14657)

Fold: Multiheme cytochromes (149)

Superfamily: Multiheme cytochromes (149)

Family: Di-heme elbow motif (53)

Protein domain: Hydroxylamine oxidoreductase, HAO (1)

Nitrosomonas europaea [TaxId: 915] (1)

1a	d1fgja_	A:
1b	d1fgjb_	B:

(no "Pfam Domain" information available for 1FGJ)

Asymmetric Unit(hide GO term definitions)

Chain A,B (HAO_NITEU | Q50925)

molecular function
	GO:0047991	hydroxylamine oxidase activity	Catalysis of the reaction: hydroxylamine + O(2) = H(2)O + H(+) + nitrite.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0019331	anaerobic respiration, using ammonium as electron donor	The oxidation of ammonium (NH4) to nitrogen (N2) in the absence of oxygen, using nitrite (NO2) as the electron acceptor. It is suggested that hydroxylamine and ammonium are combined to yield hydrazine, which is subsequently oxidized to N2.
	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 Unit
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	Cis Peptide Bonds
		Arg A:201 - Pro A:202	[ RasMol ]
		Arg B:201 - Pro B:202	[ RasMol ]
		Asn A:434 - Pro A:435	[ RasMol ]
		Asn B:434 - Pro B:435	[ RasMol ]
		Glu A:415 - Pro A:416	[ RasMol ]
		Glu B:415 - Pro B:416	[ RasMol ]

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Access by PDB/NDB ID
	1fgj
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	HAO_NITEU \| Q50925
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	1.7.3.4
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	HAO_NITEU \| Q50925	:	4fas 4n4n 4n4o

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 16)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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