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Title :   CRYSTAL STRUCTURE OF E. COLI PSEUDOURIDINE SYNTHASE RLUE

Authors :   H. Pan, J. D. Ho, R. M. Stroud, J. Finer-Moore

Date :   19 Jan 07 (Deposition) - 13 Mar 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Bifurcated Beta Sheet, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Pan, J. D. Ho, R. M. Stroud, J. Finer-Moore
The Crystal Structure Of E. Coli Rrna Pseudouridine Synthase Rlue.
J. Mol. Biol. V. 367 1459 2007
PubMed-ID: 17320904 | Reference-DOI: 10.1016/J.JMB.2007.01.084
(for further references see the PDB file header)

Molecule 1 - RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE E
	Chains	:	A, B
	EC Number	:	5.4.99.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RLUE
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	RRNA- URIDINE ISOMERASE E, RRNA PSEUDOURIDYLATE SYNTHASE E

		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 (3, 8)

No.	Name	Count	Type	Full Name
1	ACY	6	Ligand/Ion	ACETIC ACID
2	DTT	1	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	DTT	-1	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	ACY	4	Ligand/Ion	ACETIC ACID
2	DTT	1	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
3	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:53 , PHE A:54 , THR A:55 , THR A:130 , HIS A:186 , HOH A:1011 , HOH A:1014 , HOH A:1018 , HOH A:1051	BINDING SITE FOR RESIDUE SO4 A 1001
2	AC2	SOFTWARE	ARG A:40 , PRO A:68 , VAL A:69 , TRP A:212 , GLU A:214 , LEU B:51 , ARG B:60 , ARG B:80 , HOH B:1045	BINDING SITE FOR RESIDUE DTT B 218
3	AC3	SOFTWARE	LEU B:204 , ASN B:206 , HOH B:1083	BINDING SITE FOR RESIDUE ACY B 1002
4	AC4	SOFTWARE	GLN B:53 , PHE B:54 , THR B:55	BINDING SITE FOR RESIDUE ACY B 1003
5	AC5	SOFTWARE	LEU A:131 , ASN A:132 , ARG A:182 , HOH A:1022	BINDING SITE FOR RESIDUE ACY A 1004
6	AC6	SOFTWARE	TYR A:197 , ASN A:206 , HOH A:1073	BINDING SITE FOR RESIDUE ACY A 1005
7	AC7	SOFTWARE	LYS B:61 , GLY B:102 , ARG B:104 , THR B:105 , HOH B:1113	BINDING SITE FOR RESIDUE ACY B 1006
8	AC8	SOFTWARE	ARG A:97 , ASP B:145 , GLU B:146 , HOH B:1147	BINDING SITE FOR RESIDUE ACY B 1007

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

Asymmetric Unit

No.	Residues
1	Asn A:154	-	Pro A:155
2	Asn B:154	-	Pro B:155

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

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.	RLUE_ECOLI	76-90	2	A:76-90 B:76-90

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.	RLUE_ECOLI	76-90	1	A:76-90 -

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.	RLUE_ECOLI	76-90	1	- B:76-90

(no "Exon" information available for 2OLW)

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:179
 aligned with RLUE_ECOLI | P75966 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:180
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216
           RLUE_ECOLI    37 QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 216
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee...............hhhhh......ee........eeeeeee.hhhhhhhhhh......eeeeeeee...hhhhhhhhhhh.ee..ee....eeeee..............-.....eeeeeeee.....hhhhhhhhhh...eeeeeeeee..ee........eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------PSI_RSU        ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2olw A  37 QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIR-RKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 216
                                    46        56        66        76        86        96       106       116       126       136       146       156 | |   166       176       186       196       206       216
                                                                                                                                                   158 |                                                        
                                                                                                                                                     160

Chain B from PDB  Type:PROTEIN  Length:179
 aligned with RLUE_ECOLI | P75966 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:180
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217
           RLUE_ECOLI    38 PTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVTD 217
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --PseudoU_synth_2-2olwB01 B:40-186                                                                                                                   ------------------------------- Pfam domains (1)
           Pfam domains (2) --PseudoU_synth_2-2olwB02 B:40-186                                                                                                                   ------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeee...ee.........ee.hhh......ee........eeeeeee.hhhhhhhhhh......eeeeeeee...hhhhhhhhhhh.ee..ee....eeeee..............-.....eeeeeeee.....hhhhhhhhhhh..eeeeeeeee..ee........eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------PSI_RSU        ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2olw B  38 PTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIR-RKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVTD 217
                                    47        57        67        77        87        97       107       117       127       137       147       157| |    167       177       187       197       207       217
                                                                                                                                                  158 |                                                         
                                                                                                                                                    160

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 2OLW)

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

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_2-2olwB01	B:40-186
1b	PseudoU_synth_2-2olwB02	B:40-186

Asymmetric Unit(hide GO term definitions)

Chain A,B (RLUE_ECOLI | P75966)

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Asn A:154 - Pro A:155	[ RasMol ]
		Asn B:154 - Pro B:155	[ RasMol ]

Biological Units
	Complete Structure
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		Biological Unit 2	[ Jena3D ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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