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Title :   THE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PSEUDOURIDINE SYNTHASE RLUC FROM ESCHERICHIA COLI

Authors :   Y. Machida, K. Mizutani, S. Unzai, S. -Y. Park, J. R. H. Tame

Date :   26 Jan 04 (Deposition) - 18 May 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Pseudouridine Syntase, Rna Binding, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Mizutani, Y. Machida, S. Unzai, S. -Y. Park, J. R. H. Tame
Crystal Structures Of The Catalytic Domains Of Pseudouridine Synthases Rluc And Rlud From Escherichia Coli
Biochemistry V. 43 4454 2004
PubMed-ID: 15078091 | Reference-DOI: 10.1021/BI036079C
(for further references see the PDB file header)

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	:	PET21B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN
	Gene	:	RLUC
	Mutation	:	YES
	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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:142 , GLN A:185 , SER A:186 , LYS A:197 , ARG A:205 , THR A:241 , HOH A:423	BINDING SITE FOR RESIDUE SO4 A 400
2	AC2	SOFTWARE	MSE A:304 , ARG B:157 , SER B:158 , ARG B:161 , HOH B:1401	BINDING SITE FOR RESIDUE SO4 B 1400

(no "SS Bond" information available for 1V9K)

(no "Cis Peptide Bond" information available for 1V9K)

(no "SAP(SNP)/Variant" information available for 1V9K)

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

(no "Exon" information available for 1V9K)

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
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Chain A from PDB  Type:PROTEIN  Length:227
 aligned with RLUC_ECOLI | P0AA39 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:227
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       
           RLUC_ECOLI    93 DVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVMRIEAPMDEGLKRCLQKLRNAR 319
               SCOP domains d1v9ka_ A: Ribosomal large subunit pseudouridine synthase C, RluC                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeee..............hhhhhhhhhh......ee........eeeeeee.hhhhhhhhhhhhhh...eeeeeeeee........ee...eeeee.....eeeee........eeeeeeee...eeeeeeee.....hhhhhhhhhh...........hhhhhhhhhhh........eeeeeeeee......eeeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------PSI_RLU        --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v9k A  93 DVImYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGmQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVmRIEAPmDEGLKRCLQKmRNAR 319
                               |   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292     | 302 |     312  |    
                               |                                                                         172-MSE                                                                                                                       298-MSE |        315-MSE
                              96-MSE                                                                                                                                                                                                         304-MSE

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with RLUC_ECOLI | P0AA39 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:227
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       
           RLUC_ECOLI    93 DVILYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVMRIEAPMDEGLKRCLQKLRNAR 319
               SCOP domains d1v9kb_ B: Ribosomal large subunit pseudouridine synthase C, RluC                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeee..............hhhhhhhhhh......ee........eeeeeee.hhhhhhhhhhhhhh...eeeeeeeee........ee...eeeee.....eeeee........eeeeeeee...eeeeeeee.....hhhhhhhhhh...........hhhhhhhhhhh........eeeeeeeee......eeeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------PSI_RLU        --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v9k B  93 DVImYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGmQKDYLALVRGQWQSHVKSVQAPLLKNILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRCSPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDRQLTEAGTGLNRLFLHAAALKFTHPGTGEVmRIEAPmDEGLKRCLQKmRNAR 319
                               |   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292     | 302 |     312  |    
                              96-MSE                                                                     172-MSE                                                                                                                       298-MSE |        315-MSE
                                                                                                                                                                                                                                             304-MSE

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Pseudouridine synthase (30)

Superfamily: Pseudouridine synthase (30)

Family: Pseudouridine synthase RsuA/RluD (8)

Protein domain: Ribosomal large subunit pseudouridine synthase C, RluC (1)

Escherichia coli [TaxId: 562] (1)

1a	d1v9ka_	A:
1b	d1v9kb_	B:

(no "CATH Domain" information available for 1V9K)

(no "Pfam Domain" information available for 1V9K)

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.

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