1RZP - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF C-TERMINAL DESPENTAPEPTIDE NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT PH6.2

Authors :   H. T. Li, C. Wang, T. Chang, W. C. Chang, M. Y. Liu, J. Le Gall, L. L. Gui, J. P. Zhang, X. M. An, W. R. Chang

Date :   26 Dec 03 (Deposition) - 30 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Denitrification, Residue Deletion, Ph Profile, Greek Key Beta Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. T. Li, C. Wang, T. Chang, W. C. Chang, M. Y. Liu, J. Le Gall, L. L. Gui, J. P. Zhang, X. M. An, W. R. Chang
Ph-Profile Crystal Structure Studies Of C-Terminal Despentapeptide Nitrite Reductase From Achromobacter Cycloclastes
Biochem. Biophys. Res. Commun. V. 316 107 2004
PubMed-ID: 15003518 | Reference-DOI: 10.1016/J.BBRC.2004.01.177
(for further references see the PDB file header)

Molecule 1 - COPPER-CONTAINING NITRITE REDUCTASE
	Chains	:	A, B, C
	EC Number	:	1.7.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	M15(PREP4)
	Expression System Taxid	:	562
	Fragment	:	C-TERMINAL DESPENTAPEPTIDE NITRITE REDUCTASE
	Organism Scientific	:	ACHROMOBACTER CYCLOCLASTES
	Organism Taxid	:	223
	Synonym	:	CU-NIR

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	CU	6	Ligand/Ion	COPPER (II) ION
2	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:95 , CYS A:136 , HIS A:145 , MET A:150	BINDING SITE FOR RESIDUE CU A 501
02	AC2	SOFTWARE	ASP A:98 , HIS A:100 , HIS A:135 , HOH A:3003 , 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 CU B 501
04	AC4	SOFTWARE	HIS B:100 , HIS B:135 , HOH B:2003 , 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 CU C 501
06	AC6	SOFTWARE	HIS A:306 , ASP C:98 , HIS C:100 , HIS C:135 , HOH C:3002	BINDING SITE FOR RESIDUE CU C 502
07	AC7	SOFTWARE	PHE C:24 , LYS C:174 , TYR C:176 , THR C:234 , HOH C:3030 , HOH C:3168	BINDING SITE FOR RESIDUE SO4 C 3001
08	AC8	SOFTWARE	PHE A:24 , LYS A:174 , TYR A:176 , THR A:234 , HOH A:3051 , HOH A:3116 , HOH A:3205	BINDING SITE FOR RESIDUE SO4 A 3002
09	AC9	SOFTWARE	HIS C:28 , GLN C:30 , ASP C:173 , LYS C:174 , ILE C:175 , HOH C:3052 , HOH C:3170 , HOH C:3179 , HOH C:3192 , HOH C:3231	BINDING SITE FOR RESIDUE MES C 2001
10	BC1	SOFTWARE	HIS B:28 , GLN B:30 , ASP B:173 , LYS B:174 , ILE B:175 , HOH B:2018 , HOH B:2131 , HOH B:2135 , HOH B:2225 , HOH B:2249 , HOH C:3183 , HOH C:3200	BINDING SITE FOR RESIDUE MES B 2002

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

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 1RZP)

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

(no "Exon" information available for 1RZP)

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:328
 aligned with NIR_ACHCY | P25006 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:328
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365        
            NIR_ACHCY    46 DISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVV 373
               SCOP domains d1rzpa1 A:8-166 Nitrite reductase, NIR                                                                                                                         d1rzpa2 A:167-335 Nitrite reductase, NIR                                                                                                                                  SCOP domains
               CATH domains 1rzpA01 A:8-158 Cupredoxins -  blue copper proteins                                                                                                    1rzpA02 A:159-325 Cupredoxins -  blue copper proteins                                                                                                                  ---------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee.......eeeee...eeeeeeee..........ee....hhhhhh........eeeeeeee....eeeeee.....hhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rzp A   8 DISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVV 335
                                    17        27        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

Chain B from PDB  Type:PROTEIN  Length:328
 aligned with NIR_ACHCY | P25006 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:328
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365        
            NIR_ACHCY    46 DISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVV 373
               SCOP domains d1rzpb1 B:8-166 Nitrite reductase, NIR                                                                                                                         d1rzpb2 B:167-335 Nitrite reductase, NIR                                                                                                                                  SCOP domains
               CATH domains 1rzpB01 B:8-158 Cupredoxins -  blue copper proteins                                                                                                    1rzpB02 B:159-325 Cupredoxins -  blue copper proteins                                                                                                                  ---------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee.......eeeee...eeeeeeee..........ee....hhhhhh........eeeeeeee....eeeeee.....hhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee..............hhhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rzp B   8 DISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVV 335
                                    17        27        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

Chain C from PDB  Type:PROTEIN  Length:332
 aligned with NIR_ACHCY | P25006 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:332
                                    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  
            NIR_ACHCY    42 AAPVDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVV 373
               SCOP domains d1rzpc1 C:4-166 Nitrite reductase, NIR                                                                                                                             d1rzpc2 C:167-335 Nitrite reductase, NIR                                                                                                                                  SCOP domains
               CATH domains ----1rzpC01 C:8-158 Cupredoxins -  blue copper proteins                                                                                                    1rzpC02 C:159-325 Cupredoxins -  blue copper proteins                                                                                                                  ---------- CATH domains
           Pfam domains (1) ----------------------------------------Cu-oxidase_3-1rzpC04 C:44-161                                                                                         ------------Cu-oxidase-1rzpC01 C:174-326                                                                                                                             --------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------Cu-oxidase_3-1rzpC05 C:44-161                                                                                         ------------Cu-oxidase-1rzpC02 C:174-326                                                                                                                             --------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------Cu-oxidase_3-1rzpC06 C:44-161                                                                                         ------------Cu-oxidase-1rzpC03 C:174-326                                                                                                                             --------- Pfam domains (3)
         Sec.struct. author ....hhhhh.eee.....................eeeeeeeeeeeeee......eeeeeee.......eeeee...eeeeeeee..........ee....hhhhhhhhh.....eeeeeeee....eeeeee.....hhhhhhh...eeeeeee....ee.....ee...eeeeeeeeee...............hhhhhhhhhhhhh.....eeee.......hhhhheeee...eeeeeeee......eeee...eeeee.........eeee........eeeeeeee....eeeeeee.hhhhhhh...eeeeeee.......eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rzp C   4 AAPVDISTLPRVKVDLVKPPFVHAHDQVAKTGPRVVEFTMTIEEKKLVIDREGTEIHAMTFNGSVPGPLMVVHENDYVELRLINPDTNTLLHNIDFHAATGALGGGALTQVNPGEETTLRFKATKPGVFVYHCAPEGMVPWHVTSGMNGAIMVLPRDGLKDEKGQPLTYDKIYYVGEQDFYVPKDEAGNYKKYETPGEAYEDAVKAMRTLTPTHIVFNGAVGALTGDHALTAAVGERVLVVHSQANRDTRPHLIGGHGDYVWATGKFRNPPDLDQETWLIPGGTAGAAFYTFRQPGVYAYVNHNLIEAFELGAAGHFKVTGEWNDDLMTSVV 335
                                    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)

Achromobacter cycloclastes [TaxId: 223] (15)

1a	d1rzpa1	A:8-166
1b	d1rzpa2	A:167-335
1c	d1rzpb1	B:8-166
1d	d1rzpb2	B:167-335
1e	d1rzpc1	C:4-166
1f	d1rzpc2	C:167-335

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)

Achromobacter cycloclastes. Organism_taxid: 223. (5)

1a	1rzpA01	A:8-158
1b	1rzpA02	A:159-325
1c	1rzpB02	B:159-325
1d	1rzpC02	C:159-325
1e	1rzpB01	B:8-158
1f	1rzpC01	C:8-158

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Cu-oxidase (74)

Achromobacter cycloclastes (9)

1a	Cu-oxidase-1rzpC01	C:174-326
1b	Cu-oxidase-1rzpC02	C:174-326
1c	Cu-oxidase-1rzpC03	C:174-326

Family: Cu-oxidase_3 (79)

Achromobacter cycloclastes (9)

2a	Cu-oxidase_3-1rzpC04	C:44-161
2b	Cu-oxidase_3-1rzpC05	C:44-161
2c	Cu-oxidase_3-1rzpC06	C:44-161

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (NIR_ACHCY | P25006)

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

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	1rzp
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1rzq	THE SAME PROTEIN AT PH 5.0

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

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

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SCOP Domains (1, 6)

CATH Domains (1, 6)

Pfam Domains (2, 6)

Gene Ontology (9, 9)

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