2K9F - JenaLib

Title :   STRUCTURAL FEATURES OF THE COMPLEX BETWEEN THE DSBD N-TERMINAL AND THE PILB N-TERMINAL DOMAINS FROM NEISSERIA MENINGITIDIS

Authors :   M. Quinternet, P. Tsan, L. Selme, C. Jacob, S. Boschi-Muller, G. Branlant, M. Cung

Date :   09 Oct 08 (Deposition) - 19 May 09 (Release) - 01 Sep 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (10x)

Keywords :   Protein, Docking, Thioredoxin, Immunoglobulin, Dsbd, Pilb, Electron Transport, Multifunctional Enzyme, Oxidoreductase, Redox-Active Center, Transport, Cytochrome C-Type Biogenesis, Inner Membrane, Membrane, Nad, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Quinternet, P. Tsan, L. Selme-Roussel, C. Jacob, S. Boschi-Muller, G. Branlant, M. T. Cung
Formation Of The Complex Between Dsbd And Pilb N-Terminal Domains From Neisseria Meningitidis Necessitates An Adaptability Of Ndsbd.
Structure V. 17 1024 2009
PubMed-ID: 19604482 | Reference-DOI: 10.1016/J.STR.2009.05.011
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

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:144
 aligned with MSRAB_NEIMA | Q9JWM8 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:144
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172    
          MSRAB_NEIMA    33 TVPHTLSTLKTADNRPASVYLKKDKPTLIKFWASWCPLCLSELGQTEKWAQDAKFSSANLITVASPGFLHEKKDGDFQKWYAGLNYPKLPVVTDNGGTIAQSLNISVYPSWALIGKDGDVQRIVKGSINEAQALALIRDPNADL 176
               SCOP domains d2k9fa_ A: Peptide methionine sulfoxide reductase MsrA/MsrB, N-terminal domain                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh..ee....hhhhhh.....eeeee....hhhhhhhhhhhhhhhh..hhhhheeeeee..hhhhh....hhhhhhhh.......eee...hhhhhhh......eeeee.....eeeeee...hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2k9f A   1 MVPHTLSTLKTADNRPASVYLKKDKPTLIKFWASWCPLCLSELGQTEKWAQDAKFSSANLITVASPGFLHEKKDGDFQKWYAGLNYPKLPVVTDNGGTIAQSLNISVYPSWALIGKDGDVQRIVKGSINEAQALALIRDPNADL 144
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with DSBD_NEIMB | Q9JYM0 from UniProtKB/Swiss-Prot  Length:601

    Alignment length:128
                                    28        38        48        58        68        78        88        98       108       118       128       138        
           DSBD_NEIMB    19 FALDANDLLPPEKAFVPELAVADDGVNVRFRIADGYYMYQAKIVGKTDPADLLGQPSFSKGEEKEDEFFGRQTVYHHEAQVAFPYAKAVGEPYKLVLTYQGCAEAGVCYPPVDTEFDIFGNGTYHPQT 146
               SCOP domains d2k9fb_ B: Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhheeeeeee...eeeeeeee...eeee....eeeee........ee...eeee.....eeeee.....eeee........eeeeeee.eee........eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2k9f B   1 MALDANDLLPPEKAFVPELAVADDGVNVRFRIADGYYMYQAKIVGKTNPADLLGQPSFSKGEEKEDEFFGRQTVYHHEAQVAFPYAKAVGEPYKLVLTYQGSAEAGVCYPPVDTEFDIFGNGTYHPQT 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

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 (2, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 18)

NMR Structure(hide GO term definitions)

Chain A (MSRAB_NEIMA | Q9JWM8)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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:0016671	oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
	GO:0033743	peptide-methionine (R)-S-oxide reductase activity	Catalysis of the reaction: peptide-L-methionine + H(2)O + thioredoxin disulfide = peptide-L-methionine (R)-S-oxide + thioredoxin. Can act on oxidized methionine in peptide linkage with specificity for the R enantiomer. Thioredoxin disulfide is the oxidized form of thioredoxin.
	GO:0008113	peptide-methionine (S)-S-oxide reductase activity	Catalysis of the reactions: peptide-L-methionine + thioredoxin disulfide + H2O = peptide-L-methionine (S)-S-oxide + thioredoxin, and L-methionine + thioredoxin disulfide + H2O = L-methionine (S)-S-oxide + thioredoxin. Can act on oxidized methionine in peptide linkage with specificity for the S enantiomer. Thioredoxin disulfide is the oxidized form of thioredoxin.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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.
	GO:0030091	protein repair	The process of restoring a protein to its original state after damage by such things as oxidation or spontaneous decomposition of residues.
	GO:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.

Chain B (DSBD_NEIMB | Q9JYM0)

molecular function
	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: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:0047134	protein-disulfide reductase activity	Catalysis of the reaction: protein-dithiol + NAD(P)+ = protein-disulfide + NAD(P)H + H+.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0017004	cytochrome complex assembly	The aggregation, arrangement and bonding together of a cytochrome complex. A cytochrome complex is a protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions.
	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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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