1LU4 - JenaLib

Title :   1.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A SECRETED MYCOBACTERIUM TUBERCULOSIS DISULFIDE OXIDOREDUCTASE HOMOLOGOUS TO E. COLI DSBE: IMPLICATIONS FOR FUNCTIONS

Authors :   C. W. Goulding, M. I. Apostol, S. Gleiter, A. Parseghian, J. Bardwell, M. Gennaro, D. Eisenberg, Tb Structural Genomics Consortium (Tbsgc)

Date :   21 May 02 (Deposition) - 14 Oct 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.12

Chains :   Asym./Biol. Unit : A

Keywords :   Thioredoxin-Like Fold, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. W. Goulding, M. I. Apostol, S. Gleiter, A. Parseghian, J. Bardwell, M. Gennaro, D. Eisenberg
Gram-Positive Dsbe Proteins Function Differently From Gram-Negative Dsbe Homologs: A Structure To Function Analysis Of Dsbe From Mycobacterium Tuberculosis.
J. Biol. Chem. V. 279 3516 2004
PubMed-ID: 14597624 | Reference-DOI: 10.1074/JBC.M311833200
(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 (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:134
 aligned with MPT53_MYCTO | P9WG64 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:134
                                    47        57        67        77        87        97       107       117       127       137       147       157       167    
         MPT53_MYCTO     38 ADERLQFTATTLSGAPFDGASLQGKPAVLWFWTPWCPFCNAEAPSLSQVAAANPAVTFVGIATRADVGAMQSFVSKYNLNFTNLNDADGVIWARYNVPWQPAFVFYRADGTSTFVNNPTAAMSQDELSGRVAAL  171
               SCOP domains d1lu4a_ A: Soluble secreted antigen MPT53                                                                                              SCOP domains
               CATH domains 1lu4A00 A:1001-1134 Glutaredoxin                                                                                                       CATH domains
               Pfam domains Redoxin-1lu4A01 A:1001-1133                                                                                                          - Pfam domains
         Sec.struct. author hhhhhh.eee.....eee.hhhh...eeeeee...hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhh...eeee...hhhhhhh......eeeee.....eeee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lu4 A 1001 ADERLQFTATTLSGAPFDGASLQGKPAVLWFWTPWCPFCNAEAPSLSQVAAANPAVTFVGIATRADVGAMQSFVSKYNLNFTNLNDADGVIWARYNVPWQPAFVFYRADGTSTFVNNPTAAMSQDELSGRVAAL 1134
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130

Chain A from PDB  Type:PROTEIN  Length:134
 aligned with MPT53_MYCTU | P9WG65 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:134
                                    47        57        67        77        87        97       107       117       127       137       147       157       167    
         MPT53_MYCTU     38 ADERLQFTATTLSGAPFDGASLQGKPAVLWFWTPWCPFCNAEAPSLSQVAAANPAVTFVGIATRADVGAMQSFVSKYNLNFTNLNDADGVIWARYNVPWQPAFVFYRADGTSTFVNNPTAAMSQDELSGRVAAL  171
               SCOP domains d1lu4a_ A: Soluble secreted antigen MPT53                                                                                              SCOP domains
               CATH domains 1lu4A00 A:1001-1134 Glutaredoxin                                                                                                       CATH domains
               Pfam domains Redoxin-1lu4A01 A:1001-1133                                                                                                          - Pfam domains
         Sec.struct. author hhhhhh.eee.....eee.hhhh...eeeeee...hhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhh...eeee...hhhhhhh......eeeee.....eeee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lu4 A 1001 ADERLQFTATTLSGAPFDGASLQGKPAVLWFWTPWCPFCNAEAPSLSQVAAANPAVTFVGIATRADVGAMQSFVSKYNLNFTNLNDADGVIWARYNVPWQPAFVFYRADGTSTFVNNPTAAMSQDELSGRVAAL 1134
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130

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, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (9, 14)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MPT53_MYCTU | P9WG65)

molecular function
	GO:0016209	antioxidant activity	Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
	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:0003756	protein disulfide isomerase activity	Catalysis of the rearrangement of both intrachain and interchain disulfide bonds in proteins.
	GO:0015035	protein disulfide oxidoreductase activity	Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	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:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain A (MPT53_MYCTO | P9WG64)

molecular function
	GO:0016209	antioxidant activity	Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
	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:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1lu4)

	Sites
(no "Sites" information available for 1lu4)

	Cis Peptide Bonds
		Gln A:1100 - Pro A:1101	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1lu4
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	MPT53_MYCTO \| P9WG64
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	MPT53_MYCTU \| P9WG65
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description