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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MOLYBDENUM-CONTAINING NITRATE REDUCING FRAGMENT OF PICHIA ANGUSTA ASSIMILATORY NITRATE REDUCTASE
 
Authors :  K. Fischer, G. Barbier, H. -J. Hecht, R. R. Mendel, W. H. Campbell, G. Sc
Date :  21 Jan 05  (Deposition) - 30 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Flavoprotein, 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

(-) Compounds

Molecule 1 - NITRATE REDUCTASE [NADPH]
    Chains: A
    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 11-13,20-478
    Organism Scientific: PICHIA ANGUSTA
    Organism Taxid: 4905
    Synonym: ASSIMILATORY NITRATE REDUCTASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1MTV1Ligand/Ion(MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(IV)
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MTV2Ligand/Ion(MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(IV)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS 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 , ASP A:232 , 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:272BINDING SITE FOR RESIDUE MTV A1479

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1His A:63 -Pro A:64
2Lys A:235 -Pro A:236
3Lys A:309 -Pro A:310

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MOLYBDOPTERIN_EUKPS00559 Eukaryotic molybdopterin oxidoreductases signature.NIA_PICAN109-144  1A:111-146
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MOLYBDOPTERIN_EUKPS00559 Eukaryotic molybdopterin oxidoreductases signature.NIA_PICAN109-144  2A:111-146

(-) Exons   (0, 0)

(no "Exon" information available for 2BIH)

(-) Sequences/Alignments

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:453
 aligned with NIA_PICAN | P49050 from UniProtKB/Swiss-Prot  Length:859

    Alignment length:453
                                    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   
            NIA_PICAN    24 PFPVRQDSPLTEVLPTDLKTKDNFVARDPDLLRLTGSHPFNSEPPLTKLYDSGFLTPVSLHFVRNHGPVPYVPDENILDWEVSIEGMVETPYKIKLSDIMEQFDIYSTPVTMVCAGNRRKEQNMVKKGAGFNWGAAGTSTSLWTGCMLGDVIGKARPSKRARFVWMEGADNPANGAYRTCIRLSWCMDPERCIMIAYQQNGEWLHPDHGKPLRVVIPGVIGGRSVKWLKKLVVSDRPSENWYHYFDNRVLPTMVTPEMAKSDDRWWKDERYAIYDLNLQTIICKPENQQVIKISEDEYEIAGFGYNGGGVRIGRIEVSLDKGKSWKLADIDYPEDRYREAGYFRLFGGLVNVCDRMSCLCWCFWKLKVPLSELARSKDILIRGMDERMMVQPRTMYWNVTSMLNNWWYRVAIIREGESLRFEHPVVANKPGGWMDRVKAEGGDILDNNWGEVD 476
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhh............ee.......eee.hhhhhhhh....hhhhh.ee...........hhhh.eeeeee.....eeeehhhhhhhh..eeeeeeee....hhhhhhhhh...........eeeeeeeeeehhhhhhhh.......eeeeee.........eeeeehhhhh......eeeeee..ee.hhhhh...eee.....hhhh...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: A:111-146   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bih A  26 PFPVRQDSPLTEVLPTDLKTKDNFVARDPDLLRLTGSHPFNSEPPLTKLYDSGFLTPVSLHFVRNHGPVPYVPDENILDWEVSIEGMVETPYKIKLSDIMEQFDIYSTPVTMVCAGNRRKEQNMVKKGAGFNWGAAGTSTSLWTGCMLGDVIGKARPSKRARFVWMEGADNPANGAYGTCIRLSWCMDPERCIMIAYQQNGEWLHPDHGKPLRVVIPGVIGGRSVKWLKKLVVSDRPSENWYHYFDNRVLPTMVTPEMAKSDDRWWKDERYAIYDLNLQTIICKPENQQVIKISEDEYEIAGFGYNGGGVRIGRIEVSLDKGKSWKLADIDYPEDRYREAGYFRLFGGLVNVCDRMSCLCWCFWKLKVPLSELARSKDILIRGMDERMMVQPRTMYWNVTSMLNNWWYRVAIIREGESLRFEHPVVANKPGGWMDRVKAEGGDILDNNWGEVD 478
                                    35        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
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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        NIA_PICAN | P49050: 2bii

(-) Related Entries Specified in the PDB File

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