5DJG - JenaLib

Title :   STRUCTURE OF M. TUBERCULOSIS CYSQ, A PAP PHOSPHATASE WITH PAP, MG, AND LI BOUND

Authors :   A. J. Fisher, A. I. Erickson

Date :   02 Sep 15 (Deposition) - 11 Nov 15 (Release) - 02 Dec 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A

Keywords :   Cysq, Pap Phosphatase, Pap, Lithium, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. I. Erickson, R. D. Sarsam, A. J. Fisher
Crystal Structures Of Mycobacterium Tuberculosis Cysq, With Substrate And Products Bound.
Biochemistry V. 54 6830 2015
PubMed-ID: 26512869 | Reference-DOI: 10.1021/ACS.BIOCHEM.5B01000

Compounds

Molecule 1 - 3'-PHOSPHOADENOSINE 5'-PHOSPHATE PHOSPHATASE
	Chains	:	A
	EC Number	:	3.1.3.7, 3.1.3.11, 3.1.3.25
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CYSQ, MT2189
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	CYSQ, PAP PHOSPHATASE, 3'(2'),5'-BISPHOSPHATE NUCLEOTIDASE, 5-BISPHOSPHONUCLEOSIDE 3'(2')-PHOSPHOHYDROLASE, D-FRUCTOSE-1,6- BISPHOSPHATE 1-PHOSPHOHYDROLASE, DPNPASE, FRUCTOSE-1,6- BISPHOSPHATASE, FBPASE, INOSITOL-1-MONOPHOSPHATASE,IMPASE, INOSITOL- 1-PHOSPHATASE

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:73 , ASP A:91 , LEU A:93 , LI A:302 , A3P A:303 , HOH A:457 , HOH A:491	binding site for residue MG A 301
2	AC2	SOFTWARE	ASP A:91 , ASP A:94 , ASP A:212 , MG A:301 , A3P A:303	binding site for residue LI A 302
3	AC3	SOFTWARE	HIS A:-16 , GLU A:73 , ASP A:91 , LEU A:93 , ASP A:94 , GLY A:95 , THR A:96 , SER A:162 , ARG A:165 , GLY A:185 , SER A:186 , ALA A:187 , LYS A:190 , HIS A:204 , GLY A:206 , GLY A:207 , GLN A:208 , ASP A:212 , MG A:301 , LI A:302 , HOH A:424 , HOH A:445 , HOH A:449 , HOH A:457 , HOH A:473 , HOH A:479 , HOH A:480 , HOH A:481 , HOH A:501 , HOH A:562	binding site for residue A3P A 303

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...eeee......hhhhhh.eeeeeeeeehhhhhh.......eeeeeeee....eeeeeeee.....eeee............eeeeee.....hhhhhhh....eeeeee.hhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh..eee..................eeee...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5djg A -16 HHHHHDDLTDAELAADLAADAGKLLLQVRAEIGFDQPWTLGEAGDRQANSLLLRRLQAERPGDAVLSEEAHDDLARLKSDRVWIIDPLDGTREFSTPGRDDWAVHIALWRRSPEITDAAVALPARGNVVYRTDTVTSAGVPGTLRIAVSATRPPAVLHRIRQTLAIQPVSIGSAGAKAMAVIDGYVDAYLHAGGQWEWDSAAPAGVMLAAGMHASRLDGSPLRYNQLDPYLPDLLMCRAEVAPILLGAIADAWR 267
                                ||  15        25        35        45        55        65        75        85        95       105       115 ||    129       139      |153       163       173       183       193       203       213       223       233       243       253       263    
                              -12|                                                                                                       117|                     146|                                                                                                                    
                                11                                                                                                        122                      151

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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (22, 32)

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
		A3P	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		LI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5djg)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	5djg
		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
	CYSQ_MYCTO \| P9WKJ0
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	CYSQ_MYCTU \| P9WKJ1
		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)
	3.1.3.11
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc
	3.1.3.25
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc
	3.1.3.7
		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

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	CYSQ_MYCTO \| P9WKJ0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	CYSQ_MYCTU \| P9WKJ1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description