1H9X - JenaLib

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Title :   CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED FORM

Authors :   T. Sjogren, J. Hajdu

Date :   23 Mar 01 (Deposition) - 09 Aug 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Enzyme, Nitrite Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Sjogren, J. Hajdu
The Structure Of An Alternative Form Of Paracoccus Pantotrophus Cytochrome Cd1 Nitrite Reductase
J. Biol. Chem. V. 276 29450 2001
PubMed-ID: 11373294 | Reference-DOI: 10.1074/JBC.M103657200
(for further references see the PDB file header)

Molecule 1 - CYTOCHROME CD1 NITRITE REDUCTASE
	Cellular Location	:	PERIPLASM
	Chains	:	A, B
	Gene	:	NIRS
	Organism Scientific	:	PARACOCCUS PANTOTROPHUS
	Organism Taxid	:	82367
	Other Details	:	ORGANISM FORMERLY KNOWN AS THIOSPHAERA PANTOTROPHA

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	DHE	2	Ligand/Ion	HEME D
2	HEC	2	Ligand/Ion	HEME C
3	NHE	1	Ligand/Ion	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
4	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 16)

No.	Name	Count	Type	Full Name
1	DHE	4	Ligand/Ion	HEME D
2	HEC	4	Ligand/Ion	HEME C
3	NHE	2	Ligand/Ion	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
4	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:354 , LYS A:372 , LYS B:79 , HOH B:2314 , HOH B:2315	BINDING SITE FOR RESIDUE SO4 B 621
2	AC2	SOFTWARE	GLY B:70 , VAL B:71 , LEU B:72 , ARG B:73 , LYS B:74 , GLU B:241 , HOH B:2316	BINDING SITE FOR RESIDUE SO4 B 622
3	AC3	SOFTWARE	GLN A:178 , GLY B:423 , HIS B:424 , PRO B:425 , ASP B:426 , HOH B:2318	BINDING SITE FOR RESIDUE SO4 B 623
4	AC4	SOFTWARE	ARG A:64 , CYS A:65 , CYS A:68 , HIS A:69 , THR A:77 , GLY A:78 , LYS A:79 , LEU A:89 , TYR A:93 , LEU A:94 , PHE A:97 , SER A:102 , ALA A:104 , GLY A:105 , MET A:106 , PRO A:107 , TRP A:109 , HOH A:2029 , HOH A:2310 , HOH A:2311 , HOH A:2312 , HOH A:2313	BINDING SITE FOR RESIDUE HEC A 601
5	AC5	SOFTWARE	ARG A:174 , HIS A:200 , ILE A:201 , ARG A:203 , ARG A:216 , ARG A:243 , SER A:244 , ILE A:245 , TYR A:263 , ALA A:302 , ILE A:303 , HIS A:345 , ARG A:391 , PHE A:444 , GLN A:507 , THR A:554 , PHE A:557 , HOH A:2112 , HOH A:2119 , HOH A:2178 , HOH A:2209 , HOH A:2314 , HOH A:2315 , HOH A:2316 , HOH A:2317	BINDING SITE FOR RESIDUE DHE A 602
6	AC6	SOFTWARE	LYS A:372 , HOH A:2187 , ARG B:64 , CYS B:65 , CYS B:68 , HIS B:69 , THR B:77 , GLY B:78 , LYS B:79 , TYR B:93 , LEU B:94 , PHE B:97 , ILE B:98 , SER B:102 , ALA B:104 , GLY B:105 , MET B:106 , TRP B:109 , HOH B:2013 , HOH B:2037 , HOH B:2304 , HOH B:2305 , HOH B:2306	BINDING SITE FOR RESIDUE HEC B 601
7	AC7	SOFTWARE	ARG B:174 , HIS B:200 , ILE B:201 , ARG B:203 , ARG B:216 , ARG B:243 , SER B:244 , ILE B:245 , TYR B:263 , ALA B:302 , ILE B:303 , HIS B:345 , ARG B:391 , PHE B:444 , GLN B:507 , THR B:554 , GLY B:555 , PHE B:557 , HOH B:2149 , HOH B:2307 , HOH B:2309 , HOH B:2310 , HOH B:2311 , HOH B:2312 , HOH B:2313	BINDING SITE FOR RESIDUE DHE B 602
8	AC8	SOFTWARE	ASN B:108 , GLU B:114 , ALA B:176 , GLY B:177 , ASP B:194 , TYR B:197	BINDING SITE FOR RESIDUE NHE B 611

(no "SS Bond" information available for 1H9X)

Asymmetric Unit

No.	Residues
1	Trp A:264	-	Pro A:265
2	Trp B:264	-	Pro B:265

(no "SAP(SNP)/Variant" information available for 1H9X)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	NIRS_PARPN	81-160	2	A:52-131 B:52-131

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	NIRS_PARPN	81-160	4	A:52-131 B:52-131

(no "Exon" information available for 1H9X)

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:526
 aligned with NIRS_PARPN | P72181 from UniProtKB/Swiss-Prot  Length:596

    Alignment length:526
                                    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       500       510       520       530       540       550       560       570       580       590      
           NIRS_PARPN    71 APEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 596
               SCOP domains d1h9xa1 A:42-133 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase             d1h9xa2 A:134-567 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1h9xA01 A:42-135 Cytochrome c                                                                 1h9xA02 A:136-567  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhh.........hhhhhhhhhee..hhhhh........hhh.eeeeee....eeeeee.....eeeeee....eeeeee.....eeeeee...eeeeee.......eeeeee...eeeeeee.........eeeeeeee..eeeeee.....eeeeee..ee......ee....eeeeee.....eeeeee....eeeeee.....eeeeeeee....eeeeee.....eeeeee....eeeeee....eeeeeee...........eeeee...eeeeee......eeeeee............eeeeee........ee......eeee......hhhhhh.eeeee.hhh........eeeehhhhhhh......eeeeeee.....eeeeeee.......eeeeee....eeeeee.......eeeeeehhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------CYTC  PDB: A:52-131 UniProt: 81-160                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h9x A  42 APEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 567
                                    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       471       481       491       501       511       521       531       541       551       561

Chain B from PDB  Type:PROTEIN  Length:529
 aligned with NIRS_PARPN | P72181 from UniProtKB/Swiss-Prot  Length:596

    Alignment length:529
                                    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       527       537       547       557       567       577       587         
           NIRS_PARPN    68 APGAPEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 596
               SCOP domains d1h9xb1 B:39-133 N-terminal (heme c) domain of cytochrome cd1-nitrite reductase                d1h9xb2 B:134-567 C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1h9xB01 B:39-135 Cytochrome c                                                                    1h9xB02 B:136-567  [code=2.140.10.20, no name defined]                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh......hhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhee..hhhhh........hhh.eeeeee....eeeeee.....eeeeee....eeeeee.....eeeeee...eeeeee.......eeeeee...eeeeeee.........eeeeeeee..eeeeee.....eeeeee..ee......ee....eeeeee.....eeeeee....eeeeee.....eeeeeeee....eeeeee.....eeeeee....eeeeee....eeeeeee...........eeeee...eeeeee......eeeeee............eeeeee........ee......eeee......hhhhhh.eeeee.hhh.........eeehhhhhhh......eeeeeee.....eeeeeee.......eeeeee....eeeeee.......eeeeeehhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------CYTC  PDB: B:52-131 UniProt: 81-160                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h9x B  39 APGAPEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY 567
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome Bc1 Complex; Chain D, domain 2 (279)

Homologous Superfamily: Cytochrome c (279)

Paracoccus pantotrophus. Organism_taxid: 82367. (11)

1a	1h9xB01	B:39-135
1b	1h9xA01	A:42-135

Class: Mainly Beta (13760)

Architecture: 8 Propellor (110)

Topology: Methanol Dehydrogenase; Chain A (110)

Homologous Superfamily: [code=2.140.10.20, no name defined] (22)

Paracoccus pantotrophus. Organism_taxid: 82367. (11)

2a	1h9xA02	A:136-567
2b	1h9xB02	B:136-567

(no "Pfam Domain" information available for 1H9X)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NIRS_PARPN | P72181)

molecular function
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0050418	hydroxylamine reductase activity	Catalysis of the reaction: NH3 + H2O + acceptor = hydroxylamine + reduced acceptor.
	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: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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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Trp A:264 - Pro A:265	[ RasMol ]
		Trp B:264 - Pro B:265	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	1h9x
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UniProtKB/Swiss-Prot
	NIRS_PARPN \| P72181	:	1aof 1aom 1aoq 1dy7 1e2r 1gq1 1h9y 1hcm 1hj3 1hj4 1hj5 1qks

1h9y	CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED FORM COMPLEXED TO CN
1hcm	CYTOCHROME CD1 NITRITE REDUCTASE, OXIDISED FROM FROM TETRAGONAL CRYSTALS
1hj3	CYTOCHROME CD1 NITRITE REDUCTASE, DIOXYGEN COMPLEX
1hj4	CYTOCHROME CD1 NITRITE REDUCTASE, X-RAY REDUCED DIOXYGEN COMPLEX
1hj5	CYTOCHROME CD1 NITRITE REDUCTASE, REOXIDISED ENZYME

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (2, 4)

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Gene Ontology (8, 8)

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