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Title :   CRYSTAL STRUCTURE OF E. COLI TRNA PSEUDOURIDINE SYNTHASE TRUD

Authors :   U. B. Ericsson, P. Nordlund, B. M. Hallberg, Structural Proteomics I (Spine)

Date :   06 Apr 04 (Deposition) - 20 Apr 04 (Release) - 13 Jul 11 (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 Synthase, Novel Fold, Rna Modification, Trud, Structural Proteomics In Europe, Spine, Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. B. Ericsson, P. Nordlund, B. M. Hallberg
X-Ray Structure Of Trna Pseudouridine Synthase Trud Reveals An Inserted Domain With A Novel Fold
Febs Lett. V. 565 59 2004
PubMed-ID: 15135053 | Reference-DOI: 10.1016/J.FEBSLET.2004.03.085

Molecule 1 - TRNA PSEUDOURIDINE SYNTHASE D
	Chains	:	A, B
	EC Number	:	4.2.1.70
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PT73.3
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TRUD
	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 (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1SZW)

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

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0024	PS01268	Uncharacterized protein family UPF0024 signature.	TRUD_ECOLI	77-90	2	A:77-90 B:77-90
2	TRUD	PS50984	TRUD domain profile.	TRUD_ECOLI	155-303	2	A:155-303 B:155-303

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0024	PS01268	Uncharacterized protein family UPF0024 signature.	TRUD_ECOLI	77-90	1	A:77-90 -
2	TRUD	PS50984	TRUD domain profile.	TRUD_ECOLI	155-303	1	A:155-303 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0024	PS01268	Uncharacterized protein family UPF0024 signature.	TRUD_ECOLI	77-90	1	- B:77-90
2	TRUD	PS50984	TRUD domain profile.	TRUD_ECOLI	155-303	1	- B:155-303

(no "Exon" information available for 1SZW)

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:334
 aligned with TRUD_ECOLI | Q57261 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:341
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340 
           TRUD_ECOLI     1 MIEFDNLTYLHGKPQGTGLLKANPEDFVVVEDLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCARVPGKEMPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVSNRDDVEQRLIDICVKGVPNYFGAQRFGIGGSNLQGAQRWAQTNTPVRDRNKRSFWLSAARSALFNQIVAERLKKADVNQVVDGDALQLAGRGSWFVATTEELAELQRRVNDKELMITAALPGSGEWGTQREALAFEQAAVAAETELQALLVREKVEAARRAMLLYPQQLSWNWWDDVTVEIRFWLPAGSFATSVVRELINTT 341
               SCOP domains d1szwa_ A: tRNA pseudouridine synthase TruD                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...............hhh.eeeeee..........eeeeeeee...hhhhhhhhhhhhh..hhh.eee........eeeeeeeee.......hhhhh....eeeeeeeee..........eeeeeeee....hhhhhhhhhhhhhhhhee...hhhhhhhhhhhhhhhhhhhh-------hhhhhhhhhhhhhhhhhhhhhhhh............eeee.....eee.hhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhh..hhhhhhhhhhh....eeee.ee..eeeeeeeee..eeeeeeeee...hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------UPF0024       ----------------------------------------------------------------TRUD  PDB: A:155-303 UniProt: 155-303                                                                                                                -------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1szw A   1 mIEFDNLTYLHGKPQGTGLLKANPEDFVVVEDLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCARVPGKEmPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVSNRDDVEQRLIDICVKGVPNYFGAQRFGIGGSNLQGAQRWAQ-------RNKRSFWLSAARSALFNQIVAERLKKADVNQVVDGDALQLAGRGSWFVATTEELAELQRRVNDKELmITAALPGSGEWGTQREALAFEQAAVAAETELQALLVREKVEAARRAmLLYPQQLSWNWWDDVTVEIRFWLPAGSFATSVVRELINTT 341
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   |   260       270       280       290       300|      310       320       330       340 
                            |                                                                                               98-MSE                                                                           180     188                                                               254-MSE                                        301-MSE                                    
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:330
 aligned with TRUD_ECOLI | Q57261 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:340
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340
           TRUD_ECOLI     1 MIEFDNLTYLHGKPQGTGLLKANPEDFVVVEDLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCARVPGKEMPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVSNRDDVEQRLIDICVKGVPNYFGAQRFGIGGSNLQGAQRWAQTNTPVRDRNKRSFWLSAARSALFNQIVAERLKKADVNQVVDGDALQLAGRGSWFVATTEELAELQRRVNDKELMITAALPGSGEWGTQREALAFEQAAVAAETELQALLVREKVEAARRAMLLYPQQLSWNWWDDVTVEIRFWLPAGSFATSVVRELINT 340
               SCOP domains d1szwb_ B: tRNA pseudouridine synthase TruD                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) TruD-1szwB01 B:1-337                                                                                                                                                                                                                                                                                                                             --- Pfam domains (1)
           Pfam domains (2) TruD-1szwB02 B:1-337                                                                                                                                                                                                                                                                                                                             --- Pfam domains (2)
         Sec.struct. author ..hhhhh...............hhh.eeeeee..........eeeeeeeee..hhhhhhhhhhhhhh.hhh.eee........eeeeeeeee.......hhhhh....eeeeeeeee..........eeeeeeee....hhhhhhhhhhhhhhhhee...hhhhhhhhhhhhhhhhhh----------hhhhhhhhhhhhhhhhhhhhhhh............eeee.....eee.hhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhh..hhhhhhhhhhh....eeee.ee..eeeeeeeee..eeeeeeeee...hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------UPF0024       ----------------------------------------------------------------TRUD  PDB: B:155-303 UniProt: 155-303                                                                                                                ------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1szw B   1 mIEFDNLTYLHGKPQGTGLLKANPEDFVVVEDLGFEPDGEGEHILVRILKNGCNTRFVADALAKFLKIHAREVSFAGQKDKHAVTEQWLCARVPGKEmPDLSAFQLEGCQVLEYARHKRKLRLGALKGNAFTLVLREVSNRDDVEQRLIDICVKGVPNYFGAQRFGIGGSNLQGAQRW----------NKRSFWLSAARSALFNQIVAERLKKADVNQVVDGDALQLAGRGSWFVATTEELAELQRRVNDKELmITAALPGSGEWGTQREALAFEQAAVAAETELQALLVREKVEAARRAmLLYPQQLSWNWWDDVTVEIRFWLPAGSFATSVVRELINT 340
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       | -       190       200       210       220       230       240       250   |   260       270       280       290       300|      310       320       330       340
                            1-MSE                                                                                           98-MSE                                                                         178        189                                                              254-MSE                                        301-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 '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

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

Fold: Pseudouridine synthase (30)

Superfamily: Pseudouridine synthase (30)

Family: tRNA pseudouridine synthase TruD (3)

Protein domain: tRNA pseudouridine synthase TruD (3)

Escherichia coli [TaxId: 562] (3)

1a	d1szwa_	A:
1b	d1szwb_	B:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

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Clan: no clan defined [family: TruD] (4)

Family: TruD (4)

Escherichia coli (strain K12) (3)

1a	TruD-1szwB01	B:1-337
1b	TruD-1szwB02	B:1-337

Asymmetric Unit(hide GO term definitions)

Chain A,B (TRUD_ECOLI | Q57261)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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: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: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.
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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	TRUD_ECOLI \| Q57261	:	1sb7 1si7

1sb7	CRYSTAL STRUCTURE OF THE E.COLI PSEUDOURIDINE SYNTHASE TRUD
1si7	STRUCTURE OF E. COLI TRNA PSI 13 PSEUDOURIDINE SYNTHASE TRUD
af46

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