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Title :   A NEW CATALYTIC MECHANISM OF PERIPLASMIC NITRATE REDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 FROM CRYSTALLOGRAPHIC AND EPR DATA AND BASED ON DETAILED ANALYSIS OF THE SIXTH LIGAND

Authors :   S. Najmudin, P. J. Gonzalez, J. Trincao, C. Coelho, A. Mukhopadhyay, C. I. Moura, J. J. G. Moura, C. D. Brondino, M. J. Romao

Date :   28 Jun 07 (Deposition) - 18 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

Chains :   Asym./Biol. Unit : A

Keywords :   Nitrate Assimilation, Nitrogenous Acceptor, Iron, Transport, Molybdenum, Periplasmic, Disulfide Bond, Electron Transport, Iron-Sulfur, Iron- Sulfur, Metal-Binding, Dissimilatory Nitrate Reductase, Molybdopterin Cofactor, Sulfido Ligand, 4Fe-4S Cluster, Oxidoreductase, Electron Paramagnetic Resonance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Najmudin, P. J. Gonzalez, J. Trincao, C. Coelho, A. Mukhopadhyay, N. M. F. S. A. Cerqueira, C. C. Romao, I. Moura, J. J. G. Moura, C. D. Brondino, M. J. Romao
Periplasmic Nitrate Reductase Revisited: A Sulfur Atom Completes The Sixth Coordination Of The Catalytic Molybdenum.
J. Biol. Inorg. Chem. V. 13 737 2008
PubMed-ID: 18327621 | Reference-DOI: 10.1007/S00775-008-0359-6
(for further references see the PDB file header)

Molecule 1 - PERIPLASMIC NITRATE REDUCTASE
	Atcc	:	27774
	Chains	:	A
	EC Number	:	1.7.99.4
	Organism Scientific	:	DESULFOVIBRIO DESULFURICANS
	Organism Taxid	:	876

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 6)

No.	Name	Count	Type	Full Name
1	CYN	1	Ligand/Ion	CYANIDE ION
2	MGD	2	Ligand/Ion	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
3	MO	1	Ligand/Ion	MOLYBDENUM ATOM
4	NO2	1	Ligand/Ion	NITRITE ION
5	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:13 , TYR A:15 , CYS A:16 , GLY A:19 , CYS A:20 , CYS A:47 , PRO A:182 , VAL A:183	BINDING SITE FOR RESIDUE SF4 A 800
2	AC2	SOFTWARE	CYS A:140 , MGD A:811 , MGD A:812 , CYN A:813	BINDING SITE FOR RESIDUE MO A 810
3	AC3	SOFTWARE	ARG A:14 , GLN A:111 , ASN A:136 , CYS A:140 , GLN A:312 , GLN A:346 , GLU A:416 , THR A:417 , ASN A:418 , THR A:422 , ILE A:443 , GLU A:444 , ALA A:445 , PHE A:446 , PRO A:461 , ALA A:462 , PHE A:463 , SER A:615 , ARG A:617 , TRP A:622 , HIS A:623 , THR A:624 , THR A:626 , PHE A:689 , ASN A:697 , TYR A:713 , LYS A:714 , MO A:810 , MGD A:812 , CYN A:813 , HOH A:2478 , HOH A:2588	BINDING SITE FOR RESIDUE MGD A 811
4	AC4	SOFTWARE	CYS A:16 , LYS A:49 , CYS A:140 , ILE A:173 , GLY A:174 , SER A:175 , ASN A:176 , GLU A:179 , ALA A:180 , ASP A:204 , PRO A:205 , ARG A:206 , PHE A:220 , PRO A:222 , GLY A:223 , ASP A:225 , CYS A:307 , MET A:308 , GLY A:309 , ARG A:313 , GLY A:345 , GLN A:346 , THR A:614 , MET A:616 , ARG A:617 , VAL A:618 , ILE A:619 , HIS A:621 , TRP A:622 , HIS A:623 , LYS A:714 , MO A:810 , MGD A:811 , CYN A:813 , HOH A:2196 , HOH A:2199 , HOH A:2664 , HOH A:2669	BINDING SITE FOR RESIDUE MGD A 812
5	AC5	SOFTWARE	CYS A:140 , MET A:141 , GLN A:346 , ALA A:349 , MO A:810 , MGD A:811 , MGD A:812	BINDING SITE FOR RESIDUE CYN A 813
6	AC6	SOFTWARE	MET A:616 , ARG A:617 , VAL A:618 , HIS A:621 , PHE A:689	BINDING SITE FOR RESIDUE NO2 A 814

(no "SS Bond" information available for 2JIR)

Asymmetric/Biological Unit

No.	Residues
1	Trp A:551	-	Pro A:552

(no "SAP(SNP)/Variant" information available for 2JIR)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_MOW_BIS_MGD	PS51669	Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.	NAPA_DESDA	38-93	1	A:6-61

(no "Exon" information available for 2JIR)

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:720
 aligned with NAPA_DESDA | P81186 from UniProtKB/Swiss-Prot  Length:755

    Alignment length:720
                                    45        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       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755
           NAPA_DESDA    36 RPEKWVKGVCRYCGTGCGVLVGVKDGKAVAIQGDPNNHNAGLLCLKGSLLIPVLNSKERVTQPLVRRHKGGKLEPVSWDEALDLMASRFRSSIDMYGPNSVAWYGSGQCLTEESYVANKIFKGGFGTNNVDGNPRLCMASAVGGYVTSFGKDEPMGTYADIDQATCFFIIGSNTSEAHPVLFRRIARRKQVEPGVKIIVADPRRTNTSRIADMHVAFRPGTDLAFMHSMAWVIINEELDNPRFWQRYVNFMDAEGKPSDFEGYKAFLENYRPEKVAEICRVPVEQIYGAARAFAESAATMSLWCMGINQRVQGVFANNLIHNLHLITGQICRPGATSFSLTGQPNACGGVRDGGALSHLLPAGRAIPNAKHRAEMEKLWGLPEGRIAPEPGYHTVALFEALGRGDVKCMIICETNPAHTLPNLNKVHKAMSHPESFIVCIEAFPDAVTLEYADLVLPPAFWCERDGVYGCGERRYSLTEKAVDPPGQCRPTVNTLVEFARRAGVDPQLVNFRNAEDVWNEWRMVSKGTTYDFWGMTRERLRKESGLIWPCPSEDHPGTSLRYVRGQDPCVPADHPDRFFFYGKPDGRAVIWMRPAKGAAEEPDAEYPLYLTSMRVIDHWHTATMTGKVPELQKANPIAFVEINEEDAARTGIKHGDSVIVETRRDAMELPARVSDVCRPGLIAVPFFDPKKLVNKLFLDATDPVSREPEYKICAARVRKA 755
               SCOP domains d2jira2 A:4-600 Periplasmic nitrate reductase alpha chain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            d2jira1 A:601-723 Periplasmic nitrate reductase alpha chain, NapA                                                           SCOP domains
               CATH domains 2jirA01 A:4-61 ADC-like domains                           2jirA02 A:62-139,A:346-562  [code=3.40.50.740, no name defined]               2jirA03 A:140-345,A:563-594 Dimethylsulfoxide Reductase, domain 2                                                                                                                                             2jirA02 A:62-139,A:346-562  [code=3.40.50.740, no name defined]                                                                                                                                                          2jirA03 A:140-345,A:563-594     ---------------2jirA04 A:610-723  [code=2.40.40.20, no name defined]                                                              CATH domains
               Pfam domains --Molybdop_Fe4S4-2jirA02 A:6-59                         --Molybdopterin-2jirA03 A:62-504                                                                                                                                                                                                                                                                                                                                                                                                                             ----------------------------------------------------------------------------------------------------------Molydop_binding-2jirA01 A:611-717                                                                          ------ Pfam domains
         Sec.struct. author ...eeeeee........eeeeeee..eeeeeee..........hhhhhhhhhhhhh.......ee........ee.hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhh......hhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhh.eee.....hhhhhhhhhhhhhhhh...hhhhhhhheeee.......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eeeeehhhhhh..hhhhhhhhhhhhhhhhh.......eeee.....hhhhhh........ee...ee..hhhhhhhhhhhh.............hhhhhhhhhhh....eeeee..hhhhhh.hhhhhhhhhh....eeeee.....hhhhhh..eee...hhhhh.eeee....eeeee...........hhhhhhhhhhhhh..........hhhhhhhhhhhhhh.........hhhhhhhh..ee........................................eeee................eeeeee..........hhhhhhhhhh......eeeehhhhhhh......eeeeee..eeeeeeeeee......eeeee......hhhhh................eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --4FE4S_MOW_BIS_MGD  PDB: A:6-61 UniProt: 38-93           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2jir A   4 RPEKWVKGVCRYCGTGCGVLVGVKDGKAVAIQGNPNNHNAGLLCLKGSLLIPVLNSKERVTQPLVRRHKGGKLEPVSWDEALDLMASRFRSSIDMYGPNSVAWYGSGQCLTEESYVANKIFKGGFGTNNVDGNPRLCMASAVGGYVTSFGKDEPMGTYADIDQATCFFIIGSNTSEAHPVLFRRIARRKQVEPGVKIIVADPRRTNTSRIADMHVAFRPGTDLAFMHSMAWVIINEELDNPRFWQRYVNFMDAEGKPSDFEGYKAFLENYRPEKVAEICRVPVEQIYGAARAFAESAATMSLWCMGINQRVQGVFANNLIHNLHLITGQICRPGATSFSLTGQPNACGGVRDGGALSHLLPAGRAIPNAKHRAEMEKLWGLPEGRIAPEPGYHTVALFEALGRGDVKCMIICETNPAHTLPNLNKVHKAMSHPESFIVCIEAFPDAVTLEYADLVLPPAFWCERDGVYGCGERRYSLTEKAVDPPGQCRPTVNTLVEFARRAGVDPQLVNFRNAEDVWNEWRMVSKGTTYDFWGMTRERLRKESGLIWPCPSEDHPGTSLRYVRGQDPCVPADHPDRFFFYGKPDGRAVIWMRPAKGAAEEPDAEYPLYLTSMRVIDHWHTATMTGKVPELQKANPIAFVEINEEDAARTGIKHGDSVIVETRRDAMELPARVSDVCRPGLIAVPFFDPKKLVNKLFLDATDPVSREPEYKICAARVRKA 723
                                    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       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723

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(hide GO term definitions)

Chain A (NAPA_DESDA | P81186)

molecular function
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	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:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0030151	molybdenum ion binding	Interacting selectively and non-covalently with molybdenum (Mo) ions.
	GO:0008940	nitrate reductase activity	Catalysis of the reaction: nitrite + acceptor = nitrate + reduced acceptor.
	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:0006777	Mo-molybdopterin cofactor biosynthetic process	The chemical reactions and pathways resulting in the formation of the Mo-molybdopterin cofactor, essential for the catalytic activity of some enzymes. The cofactor consists of a mononuclear molybdenum (Mo) ion coordinated by one or two molybdopterin ligands.
	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: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
		Trp A:551 - Pro A:552	[ RasMol ]

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	2jir
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	NAPA_DESDA \| P81186	:	2jim 2jio 2jip 2jiq 2nap 2v3v 2v45

2jim	A NEW CATALYTIC MECHANISM OF PERIPLASMIC NITRATE REDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 FROM CRYSTALLOGRAPHIC AND EPR DATA AND BASED ON DETAILED ANALYSIS OF THE SIXTH LIGAND
2jio	A NEW CATALYTIC MECHANISM OF PERIPLASMIC NITRATE REDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 FROM CRYSTALLOGRAPHIC AND EPR DATA AND BASED ON DETAILED ANALYSIS OF THE SIXTH LIGAND
2jip	A NEW CATALYTIC MECHANISM OF PERIPLASMIC NITRATE REDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 FROM CRYSTALLOGRAPHIC AND EPR DATA AND BASED ON DETAILED ANALYSIS OF THE SIXTH LIGAND
2jiq	A NEW CATALYTIC MECHANISM OF PERIPLASMIC NITRATE REDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 FROM CRYSTALLOGRAPHIC AND EPR DATA AND BASED ON DETAILED ANALYSIS OF THE SIXTH LIGAND
2nap	DISSIMILATORY NITRATE REDUCTASE (NAP) FROM DESULFOVIBRIO DESULFURICANS
2v3v	A NEW CATALYTIC MECHANISM OF PERIPLASMIC NITRATE REDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 FROM CRYSTALLOGRAPHIC AND EPR DATA AND BASED ON DETAILED ANALYSIS OF THE SIXTH LIGAND
2v45	A NEW CATALYTIC MECHANISM OF PERIPLASMIC NITRATE REDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 FROM CRYSTALLOGRAPHIC AND EPR DATA AND BASED ON DETAILED ANALYSIS OF THE SIXTH LIGAND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (4, 4)

Pfam Domains (3, 3)

Gene Ontology (12, 12)

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