3HCH - JenaLib

Title :   STRUCTURE OF THE C-TERMINAL DOMAIN (MSRB) OF NEISSERIA MENINGITIDIS PILB (COMPLEX WITH SUBSTRATE)

Authors :   F. M. Ranaivoson, B. Kauffmann, F. Favier

Date :   06 May 09 (Deposition) - 13 Oct 09 (Release) - 09 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Pilb, Methionine Sulfoxide Reductase B, Complex With Substrate, Disulfide Bond, Electron Transport, Multifunctional Enzyme, Oxidoreductase, Redox-Active Center, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. M. Ranaivoson, F. Neiers, B. Kauffmann, S. Boschi-Muller, G. Branlant, F. Favier
Methionine Sulfoxide Reductase B Displays A High Level Of Flexibility.
J. Mol. Biol. V. 394 83 2009
PubMed-ID: 19733575 | Reference-DOI: 10.1016/J.JMB.2009.08.073

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:20 , TRP A:442 , ARG A:466 , GLY A:479 , HIS A:480 , PHE A:482 , ARG A:493 , SER A:495	BINDING SITE FOR RESIDUE RSM A 1000
02	AC2	SOFTWARE	HOH A:46 , HOH A:109 , TYR A:436 , ASP A:437 , SER A:438 , LYS A:489 , HOH B:4 , TYR B:436 , ASP B:437 , SER B:438 , ASP B:484 , LYS B:489 , P6G B:1009	BINDING SITE FOR RESIDUE RSM A 1001
03	AC3	SOFTWARE	ALA A:433 , ASP A:434 , LYS A:435 , TYR A:436 , LYS A:489 , ASP B:488 , LYS B:489	BINDING SITE FOR RESIDUE CIT A 1003
04	AC4	SOFTWARE	GLU A:456 , ARG A:465 , THR A:467 , PHE A:482 , PRO A:483 , ASP A:484	BINDING SITE FOR RESIDUE P6G A 1005
05	AC5	SOFTWARE	HOH B:110 , TRP B:442 , ARG B:466 , GLY B:479 , HIS B:480 , PHE B:482 , SER B:495 , P6G B:1008	BINDING SITE FOR RESIDUE RSM B 1000
06	AC6	SOFTWARE	PRO A:417 , GLU A:507 , HOH B:95 , ALA B:451 , VAL B:454 , THR B:455 , GLU B:456	BINDING SITE FOR RESIDUE TRS B 1002
07	AC7	SOFTWARE	THR B:389 , GLN B:394 , VAL B:423 , LYS B:502 , ALA B:512 , TYR B:514 , P6G B:1007	BINDING SITE FOR RESIDUE P6G B 1004
08	AC8	SOFTWARE	LYS B:416 , PRO B:417 , PHE B:503 , GLN B:508 , ALA B:511 , P6G B:1004	BINDING SITE FOR RESIDUE P6G B 1007
09	AC9	SOFTWARE	ARG B:465 , THR B:467 , VAL B:481 , PRO B:483 , ASP B:484 , ARG B:493 , RSM B:1000	BINDING SITE FOR RESIDUE P6G B 1008
10	BC1	SOFTWARE	SER A:438 , RSM A:1001 , SER B:438 , ASP B:484	BINDING SITE FOR RESIDUE P6G B 1009

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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:145
 aligned with MSRAB_NEIMA | Q9JWM8 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:145
                                   387       397       407       417       427       437       447       457       467       477       487       497       507       517     
          MSRAB_NEIMA   378 YKKPSDAELKRTLTEEQYQVTQNSATEYAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTRPIDAKSVTEHDDFSYNMRRTEVRSHAADSHLGHVFPDGPRDKGGLRYCINGASLKFIPLEQMDAAGYGALKSKVK 522
               SCOP domains d3hcha_ A: automated matches                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhh.......hhhhhh...eeeee.....eeee...ee.......ee....hhh.eeeeeehhhhh.eeeeee.....eeeeee...hhhhh..eeee....eeeee.hhhh...hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----MSRB  PDB: A:383-506 UniProt: 383-506                                                                                       ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hch A 378 YKKPSDAELKRTLTEEQYQVTQNSATEYAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSGSGWPSFTRPIDAKSVTEHDDFSYNMRRTEVRSHAADSHLGHVFPDGPRDKGGLRYSINGASLKFIPLEQMDAAGYGALKSKVK 522
                                   387       397       407       417       427       437       447       457       467       477       487       497       507       517

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with MSRAB_NEIMA | Q9JWM8 from UniProtKB/Swiss-Prot  Length:522

    Alignment length:145
                                   387       397       407       417       427       437       447       457       467       477       487       497       507       517     
          MSRAB_NEIMA   378 YKKPSDAELKRTLTEEQYQVTQNSATEYAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTRPIDAKSVTEHDDFSYNMRRTEVRSHAADSHLGHVFPDGPRDKGGLRYCINGASLKFIPLEQMDAAGYGALKSKVK 522
               SCOP domains d3hchb_ B: automated matches                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhh.......hhhhhh...eeeee.....eeee...ee.......ee....hhh.eeeeee..---.eeeeee.....eeeeee...hhhhh..eeee....eeeee..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----MSRB  PDB: B:383-506 UniProt: 383-506                                                                                       ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hch B 378 YKKPSDAELKRTLTEEQYQVTQNSATEYAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSGSGWPSFTRPIDAKSVTEHDDFS---RRTEVRSHAADSHLGHVFPDGPRDKGGLRYSINGASLKFIPLEQMDAAGYGALKSKVK 522
                                   387       397       407       417       427       437       447       457   |   467       477       487       497       507       517     
                                                                                                             461 465

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 (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

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