1WY7 - JenaLib

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Title :   CRYSTAL STRUCTURE OF A PUTATIVE RNA METHYLTRANSFERASE PH1948 FROM PYROCOCCUS HORIKOSHII

Authors :   Y. G. Gao, M. Yao, I. Tanaka

Date :   08 Feb 05 (Deposition) - 13 Dec 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Seven-Stranded Beta Sheet, Methyltransferase Fold, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. G. Gao, M. Yao, Z. Yong, I. Tanaka
Crystal Structure Of The Putative Rna Methyltransferase Ph1948 From Pyrococcus Horikoshii, In Complex With The Copurified S-Adenosyl-L-Homocysteine
Proteins V. 61 1141 2005
PubMed-ID: 16245322 | Reference-DOI: 10.1002/PROT.20678

Molecule 1 - HYPOTHETICAL PROTEIN PH1948
	Chains	:	A, B, C, D
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET26B
	Expression System Strain	:	B834-DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PH1948
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	OT3

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 13)

No.	Name	Count	Type	Full Name
1	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
2	SAH	4	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 4 (2, 4)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:18 , LEU A:25 , GLU A:26 , GLN A:27 , TYR A:28 , ARG A:29 , THR A:30 , GLY A:57 , ALA A:58 , GLY A:59 , THR A:60 , GLY A:61 , VAL A:62 , GLU A:79 , VAL A:80 , ASP A:105 , VAL A:106 , ASN A:119 , PHE A:133 , HOH A:1013 , HOH A:1091	BINDING SITE FOR RESIDUE SAH A 1001
2	AC2	SOFTWARE	PHE B:18 , LEU B:25 , GLU B:26 , GLN B:27 , TYR B:28 , ARG B:29 , THR B:30 , GLY B:57 , ALA B:58 , GLY B:59 , THR B:60 , VAL B:62 , LEU B:63 , GLU B:79 , VAL B:80 , ASP B:105 , VAL B:106 , ASN B:119 , PHE B:133 , HOH B:1013 , HOH B:1076	BINDING SITE FOR RESIDUE SAH B 1002
3	AC3	SOFTWARE	PHE C:18 , LEU C:25 , GLU C:26 , GLN C:27 , TYR C:28 , THR C:30 , ASP C:55 , GLY C:57 , ALA C:58 , THR C:60 , GLU C:79 , VAL C:80 , ASP C:105 , VAL C:106 , ASN C:119 , PHE C:133 , HOH C:1018 , HOH C:1063	BINDING SITE FOR RESIDUE SAH C 1003
4	AC4	SOFTWARE	PHE D:18 , LEU D:25 , GLU D:26 , GLN D:27 , TYR D:28 , ARG D:29 , THR D:30 , GLY D:57 , ALA D:58 , THR D:60 , GLY D:61 , VAL D:62 , GLU D:79 , VAL D:80 , ASP D:105 , VAL D:106 , ASN D:119 , PHE D:133 , HOH D:1039 , HOH D:1057	BINDING SITE FOR RESIDUE SAH D 1004

(no "SS Bond" information available for 1WY7)

(no "Cis Peptide Bond" information available for 1WY7)

(no "SAP(SNP)/Variant" information available for 1WY7)

(no "PROSITE Motif" information available for 1WY7)

(no "Exon" information available for 1WY7)

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:196
 aligned with O59611_PYRHO | O59611 from UniProtKB/TrEMBL  Length:207

    Alignment length:201
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 
         O59611_PYRHO     4 RKKELAIALSKLKGFKNPKVWLEQYRTPGNAASELLWLAYSLGDIEGKVVADLGAGTGVLSYGALLLGAKEVICVEVDKEAVDVLIENLGEFKGKFKVFIGDVSEFNSRVDIVIMNPPFGSQRKHADRPFLLKAFEISDVVYSIHLAKPEVRRFIEKFSWEHGFVVTHRLTTKIEIPLQFFFHRKKLERITVDIYRFSKVI 204
               SCOP domains d1wy7a1 A:4-204 Hypothetical protein PH1948                                                                                                                                                               SCOP domains
               CATH domains 1wy7A00 A:4-204 Vaccinia Virus protein VP39                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.......hhhhh....hhhhhhhhhhhhhhh......eeeee....hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh..eeeee.hhhhh.....eeee...........hhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhh.eeeeeeeeeeeee.-----.....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wy7 A   4 RKKELAIALSKLKGFKNPKVWLEQYRTPGNAASELLWLAYSLGDIEGKVVADLGAGTGVLSYGALLLGAKEVICVEVDKEAVDVLIENLGEFKGKFKVFIGDVSEFNSRVDIVImNPPFGSQRKHADRPFLLKAFEISDVVYSIHLAKPEVRRFIEKFSWEHGFVVTHRLTTKIEIP-----HRKKLERITVDIYRFSKVI 204
                                    13        23        33        43        53        63        73        83        93       103       113    |  123       133       143       153       163       173      |  -  |    193       203 
                                                                                                                                            118-MSE                                                       180   186

Chain B from PDB  Type:PROTEIN  Length:198
 aligned with O59611_PYRHO | O59611 from UniProtKB/TrEMBL  Length:207

    Alignment length:203
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201   
         O59611_PYRHO     2 MTRKKELAIALSKLKGFKNPKVWLEQYRTPGNAASELLWLAYSLGDIEGKVVADLGAGTGVLSYGALLLGAKEVICVEVDKEAVDVLIENLGEFKGKFKVFIGDVSEFNSRVDIVIMNPPFGSQRKHADRPFLLKAFEISDVVYSIHLAKPEVRRFIEKFSWEHGFVVTHRLTTKIEIPLQFFFHRKKLERITVDIYRFSKVI 204
               SCOP domains d1wy7b_ B: Hypothetical protein PH1948                                                                                                                                                                      SCOP domains
               CATH domains -1wy7B00 B:3-204 Vaccinia Virus protein VP39                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.......hhhhh....hhhhhhhhhhhhhhh......eeeee....hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh..eeeee.hhhhh.....eeee...........hhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhh.eeeeeeeeeeeeee..-----..eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wy7 B   2 mTRKKELAIALSKLKGFKNPKVWLEQYRTPGNAASELLWLAYSLGDIEGKVVADLGAGTGVLSYGALLLGAKEVICVEVDKEAVDVLIENLGEFKGKFKVFIGDVSEFNSRVDIVImNPPFGSQRKHADRPFLLKAFEISDVVYSIHLAKPEVRRFIEKFSWEHGFVVTHRLTTKIEIPLQ-----KKLERITVDIYRFSKVI 204
                            |       11        21        31        41        51        61        71        81        91       101       111      |121       131       141       151       161       171       181|     |191       201   
                            2-MSE                                                                                                             118-MSE                                                         182   188

Chain C from PDB  Type:PROTEIN  Length:201
 aligned with O59611_PYRHO | O59611 from UniProtKB/TrEMBL  Length:207

    Alignment length:207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
         O59611_PYRHO     1 MMTRKKELAIALSKLKGFKNPKVWLEQYRTPGNAASELLWLAYSLGDIEGKVVADLGAGTGVLSYGALLLGAKEVICVEVDKEAVDVLIENLGEFKGKFKVFIGDVSEFNSRVDIVIMNPPFGSQRKHADRPFLLKAFEISDVVYSIHLAKPEVRRFIEKFSWEHGFVVTHRLTTKIEIPLQFFFHRKKLERITVDIYRFSKVINSR 207
               SCOP domains d1wy7c_ C: Hypothetical protein PH1948                                                                                                                                                                          SCOP domains
               CATH domains --1wy7C00 C:3-207 Vaccinia Virus protein VP39                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.......hhhhh....hhhhhhhhhhhhhhh......eeeee....hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh..eeeee.hhhhh.....eeee...........hhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhh.eeeeeeeeeeeee.------....eeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wy7 C   1 mmTRKKELAIALSKLKGFKNPKVWLEQYRTPGNAASELLWLAYSLGDIEGKVVADLGAGTGVLSYGALLLGAKEVICVEVDKEAVDVLIENLGEFKGKFKVFIGDVSEFNSRVDIVImNPPFGSQRKHADRPFLLKAFEISDVVYSIHLAKPEVRRFIEKFSWEHGFVVTHRLTTKIEIP------RKKLERITVDIYRFSKVINSR 207
                            ||      10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      |190       200       
                            1-MSE                                                                                                              118-MSE                                                       180    187                    
                             2-MSE

Chain D from PDB  Type:PROTEIN  Length:204
 aligned with O59611_PYRHO | O59611 from UniProtKB/TrEMBL  Length:207

    Alignment length:204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
         O59611_PYRHO     1 MMTRKKELAIALSKLKGFKNPKVWLEQYRTPGNAASELLWLAYSLGDIEGKVVADLGAGTGVLSYGALLLGAKEVICVEVDKEAVDVLIENLGEFKGKFKVFIGDVSEFNSRVDIVIMNPPFGSQRKHADRPFLLKAFEISDVVYSIHLAKPEVRRFIEKFSWEHGFVVTHRLTTKIEIPLQFFFHRKKLERITVDIYRFSKVI 204
               SCOP domains d1wy7d_ D: Hypothetical protein PH1948                                                                                                                                                                       SCOP domains
               CATH domains --1wy7D00 D:3-204 Vaccinia Virus protein VP39                                                                                                                                                                CATH domains
           Pfam domains (1) -------------------------------MTS-1wy7D01 D:32-139                                                                                        ----------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------MTS-1wy7D02 D:32-139                                                                                        ----------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------MTS-1wy7D03 D:32-139                                                                                        ----------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------MTS-1wy7D04 D:32-139                                                                                        ----------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhh.......hhhhh....hhhhhhhhhhhhhhh......eeeee....hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh..eeeee.hhhhh.....eeee...........hhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhh.eeeeeeeeeeeee...........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wy7 D   1 mmTRKKELAIALSKLKGFKNPKVWLEQYRTPGNAASELLWLAYSLGDIEGKVVADLGAGTGVLSYGALLLGAKEVICVEVDKEAVDVLIENLGEFKGKFKVFIGDVSEFNSRVDIVImNPPFGSQRKHADRPFLLKAFEISDVVYSIHLAKPEVRRFIEKFSWEHGFVVTHRLTTKIEIPLQFFFHRKKLERITVDIYRFSKVI 204
                            ||      10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
                            1-MSE                                                                                                              118-MSE                                                                                  
                             2-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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: S-adenosyl-L-methionine-dependent methyltransferases (533)

Superfamily: S-adenosyl-L-methionine-dependent methyltransferases (533)

Family: Ta1320-like (2)

Protein domain: Hypothetical protein PH1948 (1)

Pyrococcus horikoshii [TaxId: 53953] (1)

1a	d1wy7a1	A:4-204
1b	d1wy7b_	B:
1c	d1wy7c_	C:
1d	d1wy7d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Pyrococcus horikoshii ot3. Organism_taxid: 70601. Strain: ot3. (1)

1a	1wy7D00	D:3-204
1b	1wy7C00	C:3-207
1c	1wy7B00	B:3-204
1d	1wy7A00	A:4-204

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: MTS (4)

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (1)

1a	MTS-1wy7D01	D:32-139
1b	MTS-1wy7D02	D:32-139
1c	MTS-1wy7D03	D:32-139
1d	MTS-1wy7D04	D:32-139

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (O59611_PYRHO | O59611)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
biological process
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.

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