1XPI - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF E. COLI PSEUDOURIDINE SYNTHASE RLUC

Authors :   M. Del Campo, J. Ofengand, R. Fenna, A. Malhotra

Date :   08 Oct 04 (Deposition) - 04 Oct 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (2x)

Keywords :   Pseudouridine Synthase, Rluc, Catalytic Domain, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Del Campo, J. Ofengand, R. Fenna, A. Malhotra
Possible Rna Binding Domains Of Rluc And Rlud
To Be Published
PubMed: search

Molecule 1 - RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE C
	Chains	:	A, B
	EC Number	:	4.2.1.70
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	SEQUENCE DATABASE RESIDUES 89-319
	Gene	:	RLUC
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	PSEUDOURIDYLATE SYNTHASE, URACIL HYDROLYASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	ACY	5	Ligand/Ion	ACETIC ACID

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	ACY	3	Ligand/Ion	ACETIC ACID

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID

Biological Unit 3 (1, 10)

No.	Name	Count	Type	Full Name
1	ACY	10	Ligand/Ion	ACETIC ACID

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:114 , ILE A:124 , ARG A:128 , LYS A:189 , HOH A:665 , HOH A:666	BINDING SITE FOR RESIDUE ACY A 401
2	AC2	SOFTWARE	ARG A:142 , TRP A:184 , GLN A:185 , SER A:186 , LYS A:197 , ILE A:199 , ARG A:205 , ARG A:225	BINDING SITE FOR RESIDUE ACY A 402
3	AC3	SOFTWARE	ASP A:144 , GLU A:204 , ARG A:205 , HIS A:242 , HOH A:580	BINDING SITE FOR RESIDUE ACY A 403
4	AC4	SOFTWARE	PRO A:303 , MET A:304 , LYS A:309 , ARG B:161 , HOH B:596	BINDING SITE FOR RESIDUE ACY B 404
5	AC5	SOFTWARE	LEU B:195 , LYS B:197 , LYS B:214 , ARG B:240 , THR B:241	BINDING SITE FOR RESIDUE ACY B 405

(no "SS Bond" information available for 1XPI)

Asymmetric Unit

No.	Residues
1	Ala A:89	-	Ala A:90

(no "SAP(SNP)/Variant" information available for 1XPI)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PSI_RLU	PS01129	Rlu family of pseudouridine synthase signature.	RLUC_ECOLI	140-154	2	A:140-154 B:140-154

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PSI_RLU	PS01129	Rlu family of pseudouridine synthase signature.	RLUC_ECOLI	140-154	1	A:140-154 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PSI_RLU	PS01129	Rlu family of pseudouridine synthase signature.	RLUC_ECOLI	140-154	1	- B:140-154

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PSI_RLU	PS01129	Rlu family of pseudouridine synthase signature.	RLUC_ECOLI	140-154	4	A:140-154 B:140-154

(no "Exon" information available for 1XPI)

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:229
 aligned with RLUC_ECOLI | P0AA39 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:231
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318 
           RLUC_ECOLI    89 AALADVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVMRIEAPMDEGLKRCLQKLRNAR 319
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.eeee...eeeeee............eehhhhhhhh..--....ee........eeeeeee.hhhhhhhhhhhhhh...eeeeeeeee........ee...eeeee.....eeeee........eeeeeeee...eeeeeeee.....hhhhhhhhhh...........hhhhhhhhhhh........eeeeeeeee......eeeee...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------PSI_RLU        --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xpi A  89 AALADVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALR--ARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVMRIEAPMDEGLKRCLQKLRNAR 319
                                    98       108       118       128  |  | 138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318 
                                                                    131  |                                                                                                                                                                                         
                                                                       134

Chain B from PDB  Type:PROTEIN  Length:229
 aligned with RLUC_ECOLI | P0AA39 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:229
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308         
           RLUC_ECOLI    89 AALADVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVMRIEAPMDEGLKRCLQKLRN 317
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------PseudoU_synth_2-1xpiB01 B:101-250                                                                                                                     ------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------PseudoU_synth_2-1xpiB02 B:101-250                                                                                                                     ------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhh.eeee...eeeeee...........ee.hhhhhhhhhh......ee........eeeeeee.hhhhhhhhhhhhhh...eeeeeeeee........eee..eeeee.....eeeee.......eeeeeeeee...eeeeeeee.....hhhhhhhhhh...........hhhhhhhhhhh........eeeeeeeee......eeeee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------PSI_RLU        ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xpi B  89 AALADVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVMRIEAPMDEGLKRCLQKLRN 317
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308

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 '\|'

(no "SCOP Domain" information available for 1XPI)

(no "CATH Domain" information available for 1XPI)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: PseudoU_synth_2] (8)

Family: PseudoU_synth_2 (8)

Escherichia coli (strain K12) (6)

1a	PseudoU_synth_2-1xpiB01	B:101-250
1b	PseudoU_synth_2-1xpiB02	B:101-250

Asymmetric Unit(hide GO term definitions)

Chain A,B (RLUC_ECOLI | P0AA39)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0019239	deaminase activity	Catalysis of the removal of an amino group from a substrate, producing ammonia (NH3).
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0009982	pseudouridine synthase activity	Catalysis of the reaction: RNA uridine = RNA pseudouridine. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5.
biological process
	GO:0009451	RNA modification	The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
	GO:0000455	enzyme-directed rRNA pseudouridine synthesis	The intramolecular conversion of uridine to pseudouridine during ribosome biogenesis where the enzyme specifies the site that becomes pseudouridylated without using a guide RNA.
	GO:0001522	pseudouridine synthesis	The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs.
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric 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
		ACY	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:89 - Ala A:90	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1xpi
		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
	RLUC_ECOLI \| P0AA39
		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)
	4.2.1.70
		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

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
	RLUC_ECOLI \| P0AA39
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	RLUC_ECOLI \| P0AA39	:	1v9k

1v9k	THE SAME PROTEIN, BUT FOUR RESIDUES SHORTER AT THE N- TERMINUS.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (9, 9)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File