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Title :   CRYSTAL STRUCTURE OF NITRATE-REDUCING FRAGMENT OF ASSIMILATORY NITRATE REDUCTASE FROM PICHIA ANGUSTA

Authors :   K. Fischer, G. Barbier, H. -J. Hecht, R. R. Mendel, W. H. Campbell, G. Schwarz

Date :   21 Jan 05 (Deposition) - 30 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Fad, Flavoprotein, Heme, Molybdenum, Nadp, Nitrate Assimilation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Fischer, G. Barbier, H. -J. Hecht, R. R. Mendel, W. H. Campbell, G. Schwarz
Structural Basis Of Eukaryotic Nitrate Reduction: Crystal Structures Of The Nitrate Reductase Active Site
Plant Cell V. 17 1167 2005
PubMed-ID: 15772287 | Reference-DOI: 10.1105/TPC.104.029694

Molecule 1 - NITRATE REDUCTASE [NADPH]
	Chains	:	A, B
	EC Number	:	1.7.1.2
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	SNAR1-PPICZB
	Expression System Strain	:	Y-11430
	Expression System Taxid	:	4922
	Expression System Vector	:	PPICZB
	Fragment	:	MOCO-BINDING DOMAIN, DIMERIZATION DOMAIN, RESIDUES 1-13,20-478
	Organism Scientific	:	PICHIA ANGUSTA
	Organism Taxid	:	4905
	Synonym	:	ASSIMILATORY NITRATE REDUCTASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 15)

No.	Name	Count	Type	Full Name
1	GOL	7	Ligand/Ion	GLYCEROL
2	MTV	2	Ligand/Ion	(MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(IV)
3	NA	2	Ligand/Ion	SODIUM ION
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	MTV	2	Ligand/Ion	(MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(IV)
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 14)

No.	Name	Count	Type	Full Name
1	GOL	8	Ligand/Ion	GLYCEROL
2	MTV	2	Ligand/Ion	(MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(IV)
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:145 , ASN A:157 , ASN A:453 , HOH A:2383	BINDING SITE FOR RESIDUE SO4 A 601
02	AC2	SOFTWARE	PRO A:64 , ASN A:66 , ARG A:89 , ARG A:144 , GLY A:155 , PHE A:156 , HOH A:2385 , HOH A:2386	BINDING SITE FOR RESIDUE SO4 A 602
03	AC3	SOFTWARE	ARG A:295 , GLY A:338 , ARG A:339 , ASP A:410	BINDING SITE FOR RESIDUE NA A 603
04	AC4	SOFTWARE	PRO B:64 , ASN B:66 , ARG B:89 , GLY B:155 , PHE B:156 , HOH B:2386 , HOH B:2387 , HOH B:2388	BINDING SITE FOR RESIDUE SO4 B 601
05	AC5	SOFTWARE	LYS B:145 , ASN B:157 , ASN B:453 , LYS B:454 , HOH B:2389	BINDING SITE FOR RESIDUE SO4 B 602
06	AC6	SOFTWARE	ARG B:295 , ARG B:339 , MET B:409 , ASP B:410 , MET B:413	BINDING SITE FOR RESIDUE NA B 603
07	AC7	SOFTWARE	HIS A:86 , PHE A:87 , VAL A:88 , ARG A:89 , HIS A:91 , MET A:137 , CYS A:139 , ALA A:140 , ASP A:195 , TYR A:202 , HIS A:233 , ARG A:238 , ILE A:245 , GLY A:246 , GLY A:247 , SER A:249 , VAL A:250 , LYS A:251 , TRP A:252 , ASN A:272 , HOH A:2395 , HOH A:2396	BINDING SITE FOR RESIDUE MTV A1479
08	AC8	SOFTWARE	HIS B:86 , PHE B:87 , VAL B:88 , ARG B:89 , HIS B:91 , MET B:137 , CYS B:139 , ALA B:140 , ASP B:195 , TYR B:202 , HIS B:233 , ARG B:238 , GLY B:246 , GLY B:247 , SER B:249 , VAL B:250 , LYS B:251 , TRP B:252 , ASN B:272 , HOH B:2186 , HOH B:2399	BINDING SITE FOR RESIDUE MTV B1479
09	AC9	SOFTWARE	LYS A:402 , ARG A:434 , ILE A:437 , ILE A:438 , GLU A:476 , HOH A:2381 , HOH A:2388 , HOH A:2389	BINDING SITE FOR RESIDUE GOL A 701
10	BC1	SOFTWARE	ALA A:160 , ASN A:312 , VAL A:450 , VAL A:451 , ALA A:452 , HOH A:2390 , HOH A:2391 , HOH A:2392	BINDING SITE FOR RESIDUE GOL A 702
11	BC2	SOFTWARE	SER A:67 , PRO A:69 , SER A:84 , LEU A:85 , HIS A:86 , HOH A:2393	BINDING SITE FOR RESIDUE GOL A 703
12	BC3	SOFTWARE	LYS B:402 , ARG B:434 , ILE B:437 , ILE B:438 , GLU B:476 , HOH B:2382 , HOH B:2391 , HOH B:2392	BINDING SITE FOR RESIDUE GOL B 701
13	BC4	SOFTWARE	GLY B:159 , ALA B:160 , ASN B:312 , VAL B:450 , VAL B:451 , ALA B:452 , HOH B:2394 , HOH B:2396	BINDING SITE FOR RESIDUE GOL B 702
14	BC5	SOFTWARE	GLY B:111 , TRP B:190 , VAL B:257 , VAL B:258 , SER B:259 , ARG B:261 , HOH B:2398	BINDING SITE FOR RESIDUE GOL B 703
15	BC6	SOFTWARE	SER B:67 , PRO B:69 , PRO B:70 , LEU B:85 , HIS B:86 , HOH B:2008	BINDING SITE FOR RESIDUE GOL B 704

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

Asymmetric Unit

No.	Residues
1	Lys A:235	-	Pro A:236
2	Lys A:309	-	Pro A:310
3	Lys B:235	-	Pro B:236
4	Lys B:309	-	Pro B:310

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MOLYBDOPTERIN_EUK	PS00559	Eukaryotic molybdopterin oxidoreductases signature.	NIA_PICAN	109-144	2	A:111-146 B:111-146

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MOLYBDOPTERIN_EUK	PS00559	Eukaryotic molybdopterin oxidoreductases signature.	NIA_PICAN	109-144	2	A:111-146 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MOLYBDOPTERIN_EUK	PS00559	Eukaryotic molybdopterin oxidoreductases signature.	NIA_PICAN	109-144	2	- B:111-146

(no "Exon" information available for 2BII)

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:415
 aligned with NIA_PICAN | P49050 from UniProtKB/Swiss-Prot  Length:859

    Alignment length:415
                                    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     
            NIA_PICAN    62 PFNSEPPLTKLYDSGFLTPVSLHFVRNHGPVPYVPDENILDWEVSIEGMVETPYKIKLSDIMEQFDIYSTPVTMVCAGNRRKEQNMVKKGAGFNWGAAGTSTSLWTGCMLGDVIGKARPSKRARFVWMEGADNPANGAYRTCIRLSWCMDPERCIMIAYQQNGEWLHPDHGKPLRVVIPGVIGGRSVKWLKKLVVSDRPSENWYHYFDNRVLPTMVTPEMAKSDDRWWKDERYAIYDLNLQTIICKPENQQVIKISEDEYEIAGFGYNGGGVRIGRIEVSLDKGKSWKLADIDYPEDRYREAGYFRLFGGLVNVCDRMSCLCWCFWKLKVPLSELARSKDILIRGMDERMMVQPRTMYWNVTSMLNNWWYRVAIIREGESLRFEHPVVANKPGGWMDRVKAEGGDILDNNWGEVD 476
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhh....hhhhh.eee.......hhhhhhh.eeeeee.....eeeehhhhhhhh..eeeeeeee....hhhhhhhhh...........eeeeeeeeeehhhhhhhhh......eeeeee.........eeeeehhhhh......eeeeee..ee.hhhhh...eee....hhhhh...eeeeeee.....hhhhhh.........hhhhhhhhhhhhhhhhh.......eeeeee.....eee....eeeeeeeee......eeeeeee.......ee.eee.hhhhhhhh..eee..eeehhhhh......eeeeeeeehhhhhh..eeeeeeee......................eeeeeeee..eeeee.........hhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------MOLYBDOPTERIN_EUK  PDB: A:111-146   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bii A  64 PFNSEPPLTKLYDSGFLTPVSLHFVRNHGPVPYVPDENILDWEVSIEGMVETPYKIKLSDIMEQFDIYSTPVTMVCAGNRRKEQNMVKKGAGFNWGAAGTSTSLWTGCMLGDVIGKARPSKRARFVWMEGADNPANGAYGTCIRLSWCMDPERCIMIAYQQNGEWLHPDHGKPLRVVIPGVIGGRSVKWLKKLVVSDRPSENWYHYFDNRVLPTMVTPEMAKSDDRWWKDERYAIYDLNLQTIICKPENQQVIKISEDEYEIAGFGYNGGGVRIGRIEVSLDKGKSWKLADIDYPEDRYREAGYFRLFGGLVNVCDRMSCLCWCFWKLKVPLSELARSKDILIRGMDERMMVQPRTMYWNVTSMLNNWWYRVAIIREGESLRFEHPVVANKPGGWMDRVKAEGGDILDNNWGEVD 478
                                    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

Chain B from PDB  Type:PROTEIN  Length:415
 aligned with NIA_PICAN | P49050 from UniProtKB/Swiss-Prot  Length:859

    Alignment length:415
                                    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     
            NIA_PICAN    62 PFNSEPPLTKLYDSGFLTPVSLHFVRNHGPVPYVPDENILDWEVSIEGMVETPYKIKLSDIMEQFDIYSTPVTMVCAGNRRKEQNMVKKGAGFNWGAAGTSTSLWTGCMLGDVIGKARPSKRARFVWMEGADNPANGAYRTCIRLSWCMDPERCIMIAYQQNGEWLHPDHGKPLRVVIPGVIGGRSVKWLKKLVVSDRPSENWYHYFDNRVLPTMVTPEMAKSDDRWWKDERYAIYDLNLQTIICKPENQQVIKISEDEYEIAGFGYNGGGVRIGRIEVSLDKGKSWKLADIDYPEDRYREAGYFRLFGGLVNVCDRMSCLCWCFWKLKVPLSELARSKDILIRGMDERMMVQPRTMYWNVTSMLNNWWYRVAIIREGESLRFEHPVVANKPGGWMDRVKAEGGDILDNNWGEVD 476
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhh....hhhhh.eee.......hhhhhhh.eeeeee.....eeeehhhhhhhh..eeeeeeee....hhhhhhhhh...........eeeeeeeeeehhhhhhhhh......eeeeee.........eeeeehhhhh......eeeeee..ee.hhhhh...eee....hhhhh...eeeeeee.....hhhhhhh........hhhhhhhhhhhhhhhhh.......eeeeee.....eee....eeeeeeeee......eeeeeee.......ee.eee.hhhhhhhh..eee..eeehhhhh......eeeeeeeehhhhhh..eeeeeeee......................eeeeeeee..eeeee.........hhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------MOLYBDOPTERIN_EUK  PDB: B:111-146   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bii B  64 PFNSEPPLTKLYDSGFLTPVSLHFVRNHGPVPYVPDENILDWEVSIEGMVETPYKIKLSDIMEQFDIYSTPVTMVCAGNRRKEQNMVKKGAGFNWGAAGTSTSLWTGCMLGDVIGKARPSKRARFVWMEGADNPANGAYGTCIRLSWCMDPERCIMIAYQQNGEWLHPDHGKPLRVVIPGVIGGRSVKWLKKLVVSDRPSENWYHYFDNRVLPTMVTPEMAKSDDRWWKDERYAIYDLNLQTIICKPENQQVIKISEDEYEIAGFGYNGGGVRIGRIEVSLDKGKSWKLADIDYPEDRYREAGYFRLFGGLVNVCDRMSCLCWCFWKLKVPLSELARSKDILIRGMDERMMVQPRTMYWNVTSMLNNWWYRVAIIREGESLRFEHPVVANKPGGWMDRVKAEGGDILDNNWGEVD 478
                                    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

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 '\|'

(no "SCOP Domain" information available for 2BII)

(no "CATH Domain" information available for 2BII)

(no "Pfam Domain" information available for 2BII)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NIA_PICAN | P49050)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	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:0043546	molybdopterin cofactor binding	Interacting selectively and non-covalently with the molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands.
	GO:0050464	nitrate reductase (NADPH) activity	Catalysis of the reaction: nitrite + NADP+ + H2O = nitrate + NADPH + 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: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:0006809	nitric oxide biosynthetic process	The chemical reactions and pathways resulting in the formation of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water.
	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.

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	Cis Peptide Bonds
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		Lys A:309 - Pro A:310	[ RasMol ]
		Lys B:235 - Pro B:236	[ RasMol ]
		Lys B:309 - Pro B:310	[ RasMol ]

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	NIA_PICAN \| P49050	:	2bih

2bih	CRYSTAL STRUCTURE OF NITRATE-REDUCING FRAGMENT OF ASSIMILATORY NITRATE REDUCTASE FROM PICHIA ANGUSTA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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