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Title :   CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF E.COLI RLUF

Authors :   S. Sunita, H. Zhenxing, J. Swaathi, M. Cygler, A. Matte, J. Sivaraman

Date :   06 Apr 06 (Deposition) - 18 Jul 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Pseudouridine Synthase, Crystal Structure, Rluf, Ribosome, Rna Modifying Enzyme, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Sunita, H. Zhenxing, J. Swaathi, M. Cygler, A. Matte, J. Sivaraman
Domain Organization And Crystal Structure Of The Catalytic Domain Of E. Coli Rluf, A Pseudouridine Synthase That Acts On 23S Rrna
J. Mol. Biol. V. 359 998 2006
PubMed-ID: 16712869 | Reference-DOI: 10.1016/J.JMB.2006.04.019
(for further references see the PDB file header)

Molecule 1 - RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE F
	Chains	:	A, B
	EC Number	:	5.4.99.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PF04
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES (-11)-225
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	RRNA-URIDINE ISOMERASE F, RRNA PSEUDOURIDYLATE SYNTHASE F

		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 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2GML)

(no "SS Bond" information available for 2GML)

(no "Cis Peptide Bond" information available for 2GML)

(no "SAP(SNP)/Variant" information available for 2GML)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PSI_RSU	PS01149	Rsu family of pseudouridine synthase signature.	RLUF_ECOLI	104-118	2	A:39-53 B:39-53

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PSI_RSU	PS01149	Rsu family of pseudouridine synthase signature.	RLUF_ECOLI	104-118	1	A:39-53 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PSI_RSU	PS01149	Rsu family of pseudouridine synthase signature.	RLUF_ECOLI	104-118	1	- B:39-53

(no "Exon" information available for 2GML)

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:175
 aligned with RLUF_ECOLI | P32684 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:175
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235     
           RLUF_ECOLI    66 DLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSS 240
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..............hhhhhh......eee.......eeeeeee.hhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhh...ee..ee....eeeeee..eeeeee.....hhhhhhhhhh...eeeeeeeee..ee........eee.hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------PSI_RSU        -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gml A   1 DLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGmSAGVPILGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRmCEHFGYEVKKLERTRImNVSLSGIPLGEWRDLTDDELIDLFKLIENSS 175
                                    10        20        30        40        50        60        70        80       |90       100       110       120      |130       140   |   150       160       170     
                                                                                                                  88-MSE                                127-MSE          144-MSE

Chain B from PDB  Type:PROTEIN  Length:175
 aligned with RLUF_ECOLI | P32684 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:175
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235     
           RLUF_ECOLI    66 DLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSS 240
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..............hhhhhh......ee........eeeeeee.hhhhhhhhhhhhh...eeeeeee....hhhhhhhhh.............eeeeee..eeeeee.....hhhhhhhhh....eeeeeeeee..ee........eee.hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------PSI_RSU        -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gml B   1 DLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGmSAGVPILGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRmCEHFGYEVKKLERTRImNVSLSGIPLGEWRDLTDDELIDLFKLIENSS 175
                                    10        20        30        40        50        60        70        80       |90       100       110       120      |130       140   |   150       160       170     
                                                                                                                  88-MSE                                127-MSE          144-MSE

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 2GML)

(no "CATH Domain" information available for 2GML)

(no "Pfam Domain" information available for 2GML)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RLUF_ECOLI | P32684)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0016866	intramolecular transferase activity	Catalysis of the transfer of a functional group from one position to another within a single molecule.
	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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		Biological Unit 2	[ Jena3D ]

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	5.4.99.-
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	RLUF_ECOLI \| P32684	:	3dh3

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