2PQ4 - JenaLib

Title :   NMR SOLUTION STRUCTURE OF NAPD IN COMPLEX WITH NAPA1-35 SIGNAL PEPTIDE

Authors :   O. M. Minailiuc, I. Ekiel, M. Milad, Montreal-Kingston Bacterial Structural Genomics Initiative (Bsgi)

Date :   01 May 07 (Deposition) - 20 May 08 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)

Keywords :   Napd/Napa1-35, Mixed Beta-Alpha Sandwich Structure, Protein- Peptide Complex, Alpha-Helix, Structural Genomics, Psi, Protein Structure Initiative, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Chaperone/Oxidoreductase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. M. Minailiuc, I. Ekiel, J. Cheng, M. Milad, S. Gandhi, R. Larocque, M. Cygler, A. Matte
Solution Structure Of Napd, A Private Chaperone Of Periplasmic Nitrate Reductase Napa/B, In Complex With Napa1-35 Signal Peptide.
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

NMR Structure

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:90
 aligned with NAPD_ECOLI | P0A9I5 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:90
                               1                                                                                      
                               |     7        17        27        37        47        57        67        77        87
            NAPD_ECOLI    - ---MHTNWQVCSLVVQAKSERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLIQTIESVRNVEGVLAVSLVYHQQEEQGEETP 87
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----NapD-2pq4A01 A:6-85                                                             ----- Pfam domains
         Sec.struct. author .........eeeeeeeehhhhhhhhhhhhhhh...eeee......eeeeeee..hhhhhhhhhhhhhhh..eeeee...ee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                  2pq4 A  1 GSHMHTNWQVCSLVVQAKSERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLIQTIESVRNVEGVLAVSLVYHQQEEQGEETP 90
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:35
 aligned with NAPA_ECOLI | P33937 from UniProtKB/Swiss-Prot  Length:828

    Alignment length:35
                                    10        20        30     
            NAPA_ECOLI    1 MKLSRRSFMKANAVAAAAAAAGLSVPGVARAVVGQ 35
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE TAT  PDB: B:1-31 UniProt: 1-31 ---- PROSITE
                 Transcript ----------------------------------- Transcript
                  2pq4 B  1 MKLSRRSFMKANAVAAAAAAAGLSVPGVARAVVGQ 35
                                    10        20        30

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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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (18, 19)

NMR Structure(hide GO term definitions)

Chain A (NAPD_ECOLI | P0A9I5)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005048	signal sequence binding	Interacting selectively and non-covalently with a signal sequence, a specific peptide sequence found on protein precursors or mature proteins that dictates where the mature protein is localized.
biological process
	GO:0051224	negative regulation of protein transport	Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B (NAPA_ECOLI | P33937)

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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0009061	anaerobic respiration	The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
	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:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	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).

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