1IM8 - JenaLib

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Title :   CRYSTAL STRUCTURE OF YECO FROM HAEMOPHILUS INFLUENZAE (HI0319), A METHYLTRANSFERASE WITH A BOUND S-ADENOSYLHOMOCYSTEINE

Authors :   K. Lim, H. Zhang, A. Tempczyk, N. Bonander, J. Toedt, A. Howard, E. Eisen O. Herzberg, Structure 2 Function Project (S2F)

Date :   10 May 01 (Deposition) - 07 Nov 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Methyltransferase, Adenosylhomocysteine, Structural Genomics, Hypothetical Protein, Structure 2 Function Project, S2F, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Lim, H. Zhang, A. Tempczyk, N. Bonander, J. Toedt, A. Howard, E. Eisenstein, O. Herzberg
Crystal Structure Of Yeco From Haemophilus Influenzae (Hi0319) Reveals A Methyltransferase Fold And A Bound S-Adenosylhomocysteine.
Proteins V. 45 397 2001
PubMed-ID: 11746687 | Reference-DOI: 10.1002/PROT.10004

Molecule 1 - YECO
	Chains	:	A, B
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PET15B
	Gene	:	HI0319
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE RD
	Organism Taxid	:	71421
	Strain	:	KW20
	Synonym	:	METHYLTRANSFERASE, HYPOTHETICAL PROTEIN HI0319

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	SAI	2	Ligand/Ion	S-ADENOSYL-L-HOMOSELENOCYSTEINE

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	SAI	1	Ligand/Ion	S-ADENOSYL-L-HOMOSELENOCYSTEINE

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	SAI	1	Ligand/Ion	S-ADENOSYL-L-HOMOSELENOCYSTEINE

Biological Unit 3 (2, 14)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	SAI	2	Ligand/Ion	S-ADENOSYL-L-HOMOSELENOCYSTEINE

Biological Unit 4 (2, 14)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	SAI	2	Ligand/Ion	S-ADENOSYL-L-HOMOSELENOCYSTEINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:198 , SAI A:302	BINDING SITE FOR RESIDUE CL A 300
2	AC2	SOFTWARE	PHE B:136 , ARG B:198 , SAI B:303	BINDING SITE FOR RESIDUE CL B 301
3	AC3	SOFTWARE	PHE A:19 , PHE A:27 , TYR A:38 , GLY A:63 , SER A:65 , ASP A:88 , ASN A:89 , MSE A:93 , ASN A:115 , ASP A:116 , ILE A:117 , ASN A:131 , CL A:300 , HOH A:418 , HOH A:424 , HOH A:457	BINDING SITE FOR RESIDUE SAI A 302
4	AC4	SOFTWARE	PHE B:19 , PHE B:27 , TYR B:38 , GLY B:63 , SER B:65 , ASP B:88 , ASN B:89 , MSE B:93 , ASN B:115 , ASP B:116 , ILE B:117 , ASN B:131 , PHE B:132 , PHE B:136 , CL B:301 , HOH B:415 , HOH B:443 , HOH B:598	BINDING SITE FOR RESIDUE SAI B 303

(no "SS Bond" information available for 1IM8)

(no "Cis Peptide Bond" information available for 1IM8)

(no "SAP(SNP)/Variant" information available for 1IM8)

(no "PROSITE Motif" information available for 1IM8)

(no "Exon" information available for 1IM8)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:225
 aligned with CMOA_HAEIN | P43985 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:225
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236     
           CMOA_HAEIN    17 FIFDENVAEVFPDMIQRSVPGYSNIITAIGMLAERFVTADSNVYDLGCSRGAATLSARRNINQPNVKIIGIDNSQPMVERCRQHIAAYHSEIPVEILCNDIRHVEIKNASMVILNFTLQFLPPEDRIALLTKIYEGLNPNGVLVLSEKFRFEDTKINHLLIDLHHQFKRANGYSELEVSQKRTALENVMRTDSIETHKVRLKNVGFSQVELWFQCFNFGSMIAVK 241
               SCOP domains d1im8a_ A: Hypothetical protein HI0319 (YecO)                                                                                                                                                                                     SCOP domains
               CATH domains 1im8A00 A:17-241 Vaccinia Virus protein VP39                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh......eeeee..hhhhhhhhhhhhhh......eeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1im8 A  17 FIFDENVAEVFPDmIQRSVPGYSNIITAIGmLAERFVTADSNVYDLGCSRGAATLSARRNINQPNVKIIGIDNSQPmVERCRQHIAAYHSEIPVEILCNDIRHVEIKNASmVILNFTLQFLPPEDRIALLTKIYEGLNPNGVLVLSEKFRFEDTKINHLLIDLHHQFKRANGYSELEVSQKRTALENVmRTDSIETHKVRLKNVGFSQVELWFQCFNFGSmIAVK 241
                                    26   |    36        46|       56        66        76        86      | 96       106       116       126|      136       146       156       166       176       186       196       206       216       226       236|    
                                        30-MSE           47-MSE                                        93-MSE                           127-MSE                                                                       205-MSE                         237-MSE

Chain B from PDB  Type:PROTEIN  Length:223
 aligned with CMOA_HAEIN | P43985 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:223
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238   
           CMOA_HAEIN    19 FDENVAEVFPDMIQRSVPGYSNIITAIGMLAERFVTADSNVYDLGCSRGAATLSARRNINQPNVKIIGIDNSQPMVERCRQHIAAYHSEIPVEILCNDIRHVEIKNASMVILNFTLQFLPPEDRIALLTKIYEGLNPNGVLVLSEKFRFEDTKINHLLIDLHHQFKRANGYSELEVSQKRTALENVMRTDSIETHKVRLKNVGFSQVELWFQCFNFGSMIAVK 241
               SCOP domains d1im8b_ B: Hypothetical protein HI0319 (YecO)                                                                                                                                                                                   SCOP domains
               CATH domains 1im8B00 B:19-241 Vaccinia Virus protein VP39                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhh......eeeeeee.hhhhhhhhhhhhhh......eeeee.hhhhh....eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhh..eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1im8 B  19 FDENVAEVFPDmIQRSVPGYSNIITAIGmLAERFVTADSNVYDLGCSRGAATLSARRNINQPNVKIIGIDNSQPmVERCRQHIAAYHSEIPVEILCNDIRHVEIKNASmVILNFTLQFLPPEDRIALLTKIYEGLNPNGVLVLSEKFRFEDTKINHLLIDLHHQFKRANGYSELEVSQKRTALENVmRTDSIETHKVRLKNVGFSQVELWFQCFNFGSmIAVK 241
                                    28 |      38        48        58        68        78        88    |   98       108       118       128       138       148       158       168       178       188       198      |208       218       228       238   
                                      30-MSE           47-MSE                                        93-MSE                           127-MSE                                                                       205-MSE                         237-MSE

Legend:		→ Mismatch	(orange background)
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	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(

)

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)

Haemophilus influenzae rd kw20. Organism_taxid: 71421. Strain: kw20. (1)

1a	1im8A00	A:17-241
1b	1im8B00	B:19-241

(no "Pfam Domain" information available for 1IM8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CMOA_HAEIN | P43985)

molecular function
	GO:1904047	S-adenosyl-L-methionine binding	Interacting selectively and non-covalently with S-adenosyl-L-methionine.
	GO:0008757	S-adenosylmethionine-dependent methyltransferase activity	Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
	GO:0016743	carboxyl- or carbamoyltransferase activity	Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor).
	GO:0016300	tRNA (uracil) methyltransferase activity	Catalysis of the transfer of a methyl group from a donor to a uracil residue in a tRNA molecule.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0030488	tRNA methylation	The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
	GO:0002098	tRNA wobble uridine modification	The process in which a uridine in position 34 of a tRNA is post-transcriptionally modified.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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Description

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Ligands, Modified Residues, Ions (3, 16)

Sites (4, 4)

SS Bonds (0, 0)

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