2I82 | PR0229 - JenaLib

Biol.Unit 1 - 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)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PSEUDOURIDINE SYNTHASE RLUA: INDIRECT SEQUENCE READOUT THROUGH PROTEIN-INDUCED RNA STRUCTURE

Authors :   C. Hoang

Date :   31 Aug 06 (Deposition) - 21 Nov 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,E  (1x)
Biol. Unit 2: B,F  (1x)
Biol. Unit 3: C,G  (1x)
Biol. Unit 4: D,H  (1x)

Keywords :   Pseudouridine Synthase, Lyase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Hoang, J. Chen, C. A. Vizthum, J. M. Kandel, C. S. Hamilton, E. G. Mueller, A. R. Ferre-D'Amare
Crystal Structure Of Pseudouridine Synthase Rlua: Indirect Sequence Readout Through Protein-Induced Rna Structure
Mol. Cell V. 24 535 2006
PubMed-ID: 17188032 | Reference-DOI: 10.1016/J.MOLCEL.2006.09.017
(for further references see the PDB file header)

*Molecule 1 - 5'- R(GPAPGPGPGPGPAPUPUPGPAPAPAPAPUPCPCPCPCP UPC)-3'**
	Chains	:	E, F, G, H
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE A
	Chains	:	A, B, C, D
	EC Number	:	4.2.1.70
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15-B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RLUA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	RRNA-URIDINE LYASE A, RRNA PSEUDOURIDYLATE SYNTHASE A

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A				E
Biological Unit 2 (1x)	:		B				F
Biological Unit 3 (1x)	:			C				G
Biological Unit 4 (1x)	:				D				H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 31)

No.	Name	Count	Type	Full Name
1	FOU	2	Ligand/Ion	(5S,6R)-5-FLUORO-6-HYDROXYDIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE
2	MSE	29	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	FOU	1	Ligand/Ion	(5S,6R)-5-FLUORO-6-HYDROXYDIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 7)

No.	Name	Count	Type	Full Name
1	FOU	-1	Ligand/Ion	(5S,6R)-5-FLUORO-6-HYDROXYDIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE
2	MSE	7	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (2, 8)

No.	Name	Count	Type	Full Name
1	FOU	1	Ligand/Ion	(5S,6R)-5-FLUORO-6-HYDROXYDIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE
2	MSE	7	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (1, 7)

No.	Name	Count	Type	Full Name
1	FOU	-1	Ligand/Ion	(5S,6R)-5-FLUORO-6-HYDROXYDIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE
2	MSE	7	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:62 , ASP A:64 , THR A:67 , TYR A:96 , LEU A:164 , ARG A:165 , LEU A:195 , N E:1208	BINDING SITE FOR RESIDUE FOU E 3001
2	AC2	SOFTWARE	ASP C:664 , THR C:667 , TYR C:696 , HIS C:762 , GLN C:763 , LEU C:764 , LEU C:795 , N G:1408	BINDING SITE FOR RESIDUE FOU G 3003

(no "SS Bond" information available for 2I82)

Asymmetric Unit

No.	Residues
1	Glu A:11	-	Pro A:12
2	Ser A:105	-	Pro A:106
3	Arg A:122	-	Pro A:123
4	Glu B:311	-	Pro B:312
5	Ser B:405	-	Pro B:406
6	Arg B:422	-	Pro B:423
7	Glu C:611	-	Pro C:612
8	Ser C:705	-	Pro C:706
9	Arg C:722	-	Pro C:723
10	Glu D:911	-	Pro D:912
11	Ser D:1005	-	Pro D:1006

(no "SAP(SNP)/Variant" information available for 2I82)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PSI_RLU	PS01129	Rlu family of pseudouridine synthase signature.	RLUA_ECOLI	60-74	4	A:60-74 B:360-374 C:660-674 D:960-974

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.	RLUA_ECOLI	60-74	1	A:60-74 - - -

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.	RLUA_ECOLI	60-74	1	- B:360-374 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PSI_RLU	PS01129	Rlu family of pseudouridine synthase signature.	RLUA_ECOLI	60-74	1	- - C:660-674 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PSI_RLU	PS01129	Rlu family of pseudouridine synthase signature.	RLUA_ECOLI	60-74	1	- - - D:960-974

(no "Exon" information available for 2I82)

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:217
 aligned with RLUA_ECOLI | P0AA37 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:217
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       
          RLUA_ECOLI      3 MENYNPPQEPWLVILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEARAMAPRLLLHAEMLTITHPAYGNSMTFKAPADF  219
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee...eeeeee..........hhhhh.hhhhhhhhhh...ee........eeeeeee.hhhhhhhhhhhhhh...eeeeeeeee......eeeee..eee.hhhh..eee........eeeeeeeeee...eeeeeeee.....hhhhhhhhhh...........hhhhhhh.....eeeeeeeee......eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------PSI_RLU        ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i82 A    3 mENYNPPQEPWLVILYQDDHImVVNKPSGLLSVPGRLEEHKDSVmTRIQRDYPQAESVHRLDmATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHmLALGHPILGDRFYASPEARAmAPRLLLHAEmLTITHPAYGNSmTFKAPADF  219
                            |       12        22 |      32        42    |   52        62  |     72        82        92       102       112       122       132       142       152       162     | 172       182      |192      |202       212       
                            |                   24-MSE                 47-MSE            65-MSE                                                                                                168-MSE              189-MSE   199-MSE     211-MSE    
                            3-MSE

Chain B from PDB  Type:PROTEIN  Length:214
 aligned with RLUA_ECOLI | P0AA37 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:214
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215    
          RLUA_ECOLI      6 YNPPQEPWLVILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEARAMAPRLLLHAEMLTITHPAYGNSMTFKAPADF  219
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee...eeeeee..........hhhhh.hhhhhhhh.....ee........eeeeeee.hhhhhhhhhhhhhh...eeeeeeeee......eeee...eee.hhhh..eee.........eeeeeeeee...eeeeeeee.....hhhhhhhhhh...........hhhhhhh.....eeeeeeeee......eeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------PSI_RLU        ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i82 B  306 YNPPQEPWLVILYQDDHImVVNKPSGLLSVPGRLEEHKDSVmTRIQRDYPQAESVHRLDmATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHmLALGHPILGDRFYASPEARAmAPRLLLHAEmLTITHPAYGNSmTFKAPADF  519
                                   315       325       335       345 |     355       365       375       385       395       405       415       425       435       445       455       465  |    475       485   |   495   |   505     | 515    
                                            324-MSE                347-MSE           365-MSE                                                                                                468-MSE              489-MSE   499-MSE     511-MSE

Chain C from PDB  Type:PROTEIN  Length:215
 aligned with RLUA_ECOLI | P0AA37 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:215
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214     
          RLUA_ECOLI      5 NYNPPQEPWLVILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEARAMAPRLLLHAEMLTITHPAYGNSMTFKAPADF  219
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee...eeeeee..........hhhhh.hhhhhhhh.....ee........eeeeeee.hhhhhhhhhhhhhh...eeeeeeeee......eeeee..eee.hhhh..eee........eeeeeeeeee...eeeeeeee.....hhhhhhhhhhh..........hhhhhhh.....eeeeeeeee......eeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------PSI_RLU        ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i82 C  605 NYNPPQEPWLVILYQDDHImVVNKPSGLLSVPGRLEEHKDSVmTRIQRDYPQAESVHRLDmATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHmLALGHPILGDRFYASPEARAmAPRLLLHAEmLTITHPAYGNSmTFKAPADF  819
                                   614       624       634       644  |    654       664|      674       684       694       704       714       724       734       744       754       764   |   774       784    |  794    |  804      |814     
                                             624-MSE                647-MSE           665-MSE                                                                                                768-MSE              789-MSE   799-MSE     811-MSE

Chain D from PDB  Type:PROTEIN  Length:216
 aligned with RLUA_ECOLI | P0AA37 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:216
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213      
          RLUA_ECOLI      4 ENYNPPQEPWLVILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFYASPEARAMAPRLLLHAEMLTITHPAYGNSMTFKAPADF  219
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeee...eeeeee..........hhhhh.hhhhhhh......ee........eeeeeee.hhhhhhhhhhhhhh...eeeeeeeee......eeeee..eee.hhhh..eee........eeeeeeeeee...eeeeeeee.....hhhhhhhhhhh..........hhhhhh......eeeeeeeee......eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------PSI_RLU        ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2i82 D  904 ENYNPPQEPWLVILYQDDHImVVNKPSGLLSVPGRLEEHKDSVmTRIQRDYPQAESVHRLDmATSGVIVVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLICDWPNRPKQKVCYETGKPAQTEYEVVEYAADNTARVVLKPITGRSHQLRVHmLALGHPILGDRFYASPEARAmAPRLLLHAEmLTITHPAYGNSmTFKAPADF 1119
                                   913       923|      933       943   |   953       963 |     973       983       993      1003      1013      1023      1033      1043      1053      1063    | 1073      1083     |1093     |1103      1113      
                                              924-MSE                947-MSE           965-MSE                                                                                               1068-MSE             1089-MSE  1099-MSE    1111-MSE

Chain E from PDB  Type:RNA  Length:20
                                                     
                2i82 E 1201 GAGGGGAUGAAAAUCCCCUC 1221
                                  1211      1221
                               1207|            
                                1209

Chain F from PDB  Type:RNA  Length:20
                                                     
                2i82 F 1301 GAGGGGAUGAAAAUCCCCUC 1321
                                  1311      1321
                               1307|            
                                1309

Chain G from PDB  Type:RNA  Length:20
                                                     
                2i82 G 1401 GAGGGGAUGAAAAUCCCCUC 1421
                                  1411      1421
                               1407|            
                                1409

Chain H from PDB  Type:RNA  Length:20
                                                     
                2i82 H 1501 GAGGGGAUGAAAAUCCCCUC 1521
                                  1511      1521
                               1507|            
                                1509

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 2I82)

(no "CATH Domain" information available for 2I82)

(no "Pfam Domain" information available for 2I82)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RLUA_ECOLI | P0AA37)

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.
	GO:0031118	rRNA pseudouridine synthesis	The intramolecular conversion of uridine to pseudouridine in an rRNA molecule.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
	GO:0031119	tRNA pseudouridine synthesis	The intramolecular conversion of uridine to pseudouridine in a tRNA molecule.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Arg A:122 - Pro A:123	[ RasMol ]
		Arg B:422 - Pro B:423	[ RasMol ]
		Arg C:722 - Pro C:723	[ RasMol ]
		Glu A:11 - Pro A:12	[ RasMol ]
		Glu B:311 - Pro B:312	[ RasMol ]
		Glu C:611 - Pro C:612	[ RasMol ]
		Glu D:911 - Pro D:912	[ RasMol ]
		Ser A:105 - Pro A:106	[ RasMol ]
		Ser B:405 - Pro B:406	[ RasMol ]
		Ser C:705 - Pro C:706	[ RasMol ]
		Ser D:1005 - Pro D:1006	[ RasMol ]

Biological Units
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Access by PDB/NDB ID
	2i82
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	RLUA_ECOLI \| P0AA37
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 31)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (11, 11)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

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Gene Ontology (11, 11)

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