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Title :   CRYSTAL STRUCTURE OF HUMAN PUS10, A NOVEL PSEUDOURIDINE SYNTHASE.

Authors :   C. J. Mccleverty, M. Hornsby, G. Spraggon, A. Kreusch

Date :   23 Aug 07 (Deposition) - 09 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Pseudouridine Synthase, Pus10, Rna Modification, Thump Domain, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. J. Mccleverty, M. Hornsby, G. Spraggon, A. Kreusch
Crystal Structure Of Human Pus10, A Novel Pseudouridine Synthase.
J. Mol. Biol. V. 373 1243 2007
PubMed-ID: 17900615 | Reference-DOI: 10.1016/J.JMB.2007.08.053

Molecule 1 - UNCHARACTERIZED PROTEIN FLJ32312
	Chains	:	A
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell Line	:	SF9
	Expression System Plasmid	:	PFASTBAC
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PSEUDOURIDINE SYNTHASE
	Tissue	:	PROSTATE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 8)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3	GOL	1	Ligand/Ion	GLYCEROL
4	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:447 , ILE A:486 , LYS A:487 , EPE A:1534 , HOH A:2206	BINDING SITE FOR RESIDUE CL A1529
2	AC2	SOFTWARE	GLY A:341 , ARG A:354 , HOH A:2265	BINDING SITE FOR RESIDUE CL A1530
3	AC3	SOFTWARE	ASN A:385 , HOH A:2091	BINDING SITE FOR RESIDUE CL A1531
4	AC4	SOFTWARE	VAL A:146 , LYS A:183 , LYS A:187	BINDING SITE FOR RESIDUE CL A1532
5	AC5	SOFTWARE	CYS A:21 , CYS A:24 , CYS A:109 , CYS A:112	BINDING SITE FOR RESIDUE ZN A1533
6	AC6	SOFTWARE	ARG A:342 , GLU A:343 , ASP A:344 , ARG A:452 , ARG A:457 , GLY A:483 , THR A:484 , TYR A:485 , CL A:1529 , HOH A:2206 , HOH A:2316	BINDING SITE FOR RESIDUE EPE A1534
7	AC7	SOFTWARE	ASN A:254 , TRP A:419 , HIS A:473 , LEU A:512	BINDING SITE FOR RESIDUE EPE A1535
8	AC8	SOFTWARE	THR A:18 , ASN A:110 , PRO A:268 , PRO A:269 , ASN A:270 , HOH A:2140	BINDING SITE FOR RESIDUE GOL A1536

(no "SS Bond" information available for 2V9K)

(no "Cis Peptide Bond" information available for 2V9K)

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_035617	T	484	I	PUS10_HUMAN	Unclassified	---	A	T	484	I
2	CancerSNP	VAR_PUS10_HUMAN_CCDS1865_1_01 *	T	484	I	PUS10_HUMAN	Disease (Colorectal cancer)	---	A	T	484	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2V9K)

Asymmetric/Biological Unit (17, 17)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000316752	1a	ENSE00001762293	chr2:61245389-61245143	247	PUS10_HUMAN	-	0	0	-	-
1.4	ENST00000316752	4	ENSE00001275744	chr2:61239040-61238900	141	PUS10_HUMAN	1-42	42	1	A:1-42	42
1.6b	ENST00000316752	6b	ENSE00001275720	chr2:61236150-61235896	255	PUS10_HUMAN	43-127	85	1	A:43-127 (gaps)	85
1.7	ENST00000316752	7	ENSE00001275715	chr2:61233778-61233692	87	PUS10_HUMAN	128-156	29	1	A:128-156	29
1.8	ENST00000316752	8	ENSE00001275706	chr2:61198692-61198658	35	PUS10_HUMAN	157-168	12	1	A:157-168	12
1.9	ENST00000316752	9	ENSE00001069909	chr2:61194748-61194637	112	PUS10_HUMAN	168-205	38	1	A:168-205	38
1.10	ENST00000316752	10	ENSE00001069919	chr2:61192619-61192558	62	PUS10_HUMAN	206-226	21	1	A:206-226	21
1.11	ENST00000316752	11	ENSE00001275771	chr2:61192238-61192193	46	PUS10_HUMAN	226-241	16	1	A:226-233	8
1.12	ENST00000316752	12	ENSE00001069908	chr2:61190025-61189961	65	PUS10_HUMAN	242-263	22	1	A:244-263	20
1.13	ENST00000316752	13	ENSE00001069915	chr2:61188683-61188598	86	PUS10_HUMAN	263-292	30	1	A:263-292	30
1.14	ENST00000316752	14	ENSE00001069914	chr2:61187652-61187527	126	PUS10_HUMAN	292-334	43	1	A:292-334	43
1.15	ENST00000316752	15	ENSE00001069925	chr2:61182209-61182153	57	PUS10_HUMAN	334-353	20	1	A:334-353	20
1.16	ENST00000316752	16	ENSE00001069912	chr2:61181293-61181217	77	PUS10_HUMAN	353-378	26	1	A:353-378	26
1.17	ENST00000316752	17	ENSE00001069910	chr2:61181123-61181068	56	PUS10_HUMAN	379-397	19	1	A:379-397	19
1.18	ENST00000316752	18	ENSE00001069921	chr2:61180249-61180132	118	PUS10_HUMAN	397-436	40	1	A:397-436	40
1.19	ENST00000316752	19	ENSE00001069924	chr2:61175320-61175178	143	PUS10_HUMAN	437-484	48	1	A:437-484	48
1.20	ENST00000316752	20	ENSE00001069923	chr2:61172243-61172144	100	PUS10_HUMAN	484-517	34	1	A:484-517	34
1.21b	ENST00000316752	21b	ENSE00001275765	chr2:61169568-61169104	465	PUS10_HUMAN	518-529	12	1	A:518-528	11

Asymmetric/Biological 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:467
 aligned with PUS10_HUMAN | Q3MIT2 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:529
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519         
          PUS10_HUMAN     - -MFPLTEENKHVAQLLLNTGTCPRCIFRFCGVDFHAPYKLPYKELLNELQKFLETEKDELILEVMNPPPKKIRLQELEDSIDNLSQNGEGRISVSHVGSTASKNSNLNVCNVCLGILQEFCEKDFIKKVCQKVEASGFEFTSLVFSVSFPPQLSVREHAAWLLVKQEMGKQSLSLGRDDIVQLKEAYKWITHPLFSEELGVPIDGKSLFEVSVVFAHPETVEDCHFLAAICPDCFKPAKNKQSVFTRMAVMKALNKIKEEDFLKQFPCPPNSPKAVCAVLEIECAHGAVFVAGRYNKYSRNLPQTPWIIDGERKLESSVEELISDHLLAVFKAESFNFSSSGREDVDVRTLGNGRPFAIELVNPHRVHFTSQEIKELQQKINNSSNKIQVRDLQLVTREAIGHMKEGEEEKTKTYSALIWTNKAIQKKDIEFLNDIKDLKIDQKTPLRVLHRRPLAVRARVIHFMETQYVDEHHFRLHLKTQAGTYIKEFVHGDFGRTKPNIGSLMNVTADILELDVESVDVDWPPALD 528
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.----------------------------------------------------..........hhhhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhh........eeeeeeeehhhhhhhhhhhhh.....----------.hhhhhhhhhhhhhhhhhhhhh...........eeeeeeeee..eeeeeeeee....................hhhhhhhhhhhhhhh..eeeeee........eeeeeeeeeeeeee.......hhhhhhhhhhhhhh....eeeeeeeee.hhhhhhhhhhhhhh.eeeeeeeee....hhhhhhhhhhh..eeeeee.hhhhh......eeeeeeeeeeeeeee..eeeeeeee....hhhhhhhh....ee.hhhhhhh..eeeeeeeeeee......... Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I-------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I-------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) -Exon 1.4  PDB: A:1-42 UniProt: 1-42       Exon 1.6b  PDB: A:43-127 (gaps) UniProt: 43-127                                      Exon 1.7  PDB: A:128-156     Exon 1.8    -------------------------------------Exon 1.10            ---------------Exon 1.12 [INCOMPLETE]----------------------------Exon 1.14  PDB: A:292-334 UniProt: 292-334 ------------------Exon 1.16  PDB: A:353-378 Exon 1.17          ---------------------------------------Exon 1.19  PDB: A:437-484 UniProt: 437-484      ---------------------------------Exon 1.21b  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:168-205              --------------------Exon 1.11       ---------------------Exon 1.13  PDB: A:263-292     -----------------------------------------Exon 1.15           -------------------------------------------Exon 1.18  PDB: A:397-436               -----------------------------------------------Exon 1.20  PDB: A:484-517         ----------- Transcript 1 (2)
                 2v9k A   0 GMFPLTEENKHVAQLLLNTGTCPRCIFRFCGVDFHAPYKLPYKELLNELQKFLET----------------------------------------------------NVCNVCLGILQEFCEKDFIKKVCQKVEASGFEFTSLVFSVSFPPQLSVREHAAWLLVKQEMGKQSLSLGRDDIVQLKEAYKWITHPLFSEELGVPIDGKSLFEVSVVFAHPETVEDCHFLAAICPDC----------FTRMAVMKALNKIKEEDFLKQFPCPPNSPKAVCAVLEIECAHGAVFVAGRYNKYSRNLPQTPWIIDGERKLESSVEELISDHLLAVFKAESFNFSSSGREDVDVRTLGNGRPFAIELVNPHRVHFTSQEIKELQQKINNSSNKIQVRDLQLVTREAIGHMKEGEEEKTKTYSALIWTNKAIQKKDIEFLNDIKDLKIDQKTPLRVLHRRPLAVRARVIHFMETQYVDEHHFRLHLKTQAGTYIKEFVHGDFGRTKPNIGSLMNVTADILELDVESVDVDWPPALD 528
                                     9        19        29        39        49    |    -         -         -         -         -       109       119       129       139       149       159       169       179       189       199       209       219       229   |     -    |  249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519         
                                                                                 54                                                  107                                                                                                                           233        244

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 2V9K)

(no "CATH Domain" information available for 2V9K)

(no "Pfam Domain" information available for 2V9K)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PUS10_HUMAN | Q3MIT2)

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.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (0, 0)

Exons (17, 17)

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Gene Ontology (6, 6)

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