1KYW - JenaLib

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Title :   CRYSTAL STRUCTURE ANALYSIS OF CAFFEIC ACID/5-HYDROXYFERULIC ACID 3/5-O-METHYLTRANSFERASE IN COMPLEX WITH 5-HYDROXYCONIFERALDEHYDE

Authors :   C. Zubieta, P. Kota, J. -L. Ferrer, R. A. Dixon, J. P. Noel

Date :   06 Feb 02 (Deposition) - 28 Aug 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,C,F
Biol. Unit 1: A,F  (1x)
Biol. Unit 2: C  (2x)

Keywords :   O-Methyltransferase, Lignification, Protein-Ligand Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Zubieta, P. Kota, J. L. Ferrer, R. A. Dixon, J. P. Noel
Structural Basis For The Modulation Of Lignin Monomer Methylation By Caffeic Acid/5-Hydroxyferulic Acid 3/5-O-Methyltransferase.
Plant Cell V. 14 1265 2002
PubMed-ID: 12084826 | Reference-DOI: 10.1105/TPC.001412
(for further references see the PDB file header)

Molecule 1 - CAFFEIC ACID 3-O-METHYLTRANSFERASE
	Chains	:	A, C, F
	EC Number	:	2.1.1.68
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	MEDICAGO SATIVA
	Organism Taxid	:	3879
	Synonym	:	COMT

		1	2	3
Asymmetric Unit	:	A	C	F
Biological Unit 1 (1x)	:	A		F
Biological Unit 2 (2x)	:		C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	HFL	1	Ligand/Ion	5-(3,3-DIHYDROXYPROPENY)-3-METHOXY-BENZENE-1,2-DIOL
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	HFL	1	Ligand/Ion	5-(3,3-DIHYDROXYPROPENY)-3-METHOXY-BENZENE-1,2-DIOL
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	HFL	-1	Ligand/Ion	5-(3,3-DIHYDROXYPROPENY)-3-METHOXY-BENZENE-1,2-DIOL
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY C:208 , ASP C:231 , LEU C:232 , ASP C:251 , MET C:252 , PHE C:253 , LYS C:265 , TRP C:266 , TRP C:271 , HOH C:1713	BINDING SITE FOR RESIDUE SAH C 1698
2	AC2	SOFTWARE	SER F:184 , GLY F:208 , ASP F:231 , LEU F:232 , GLY F:250 , ASP F:251 , MET F:252 , PHE F:253 , LYS F:265 , TRP F:266 , TRP F:271 , HOH F:1743 , HOH F:1766 , HOH F:1767	BINDING SITE FOR RESIDUE SAH F 1699
3	AC3	SOFTWARE	LEU F:136 , ALA F:162 , MET F:180 , ASP F:270 , MET F:320 , HIS F:323 , ASN F:324 , HOH F:1714	BINDING SITE FOR RESIDUE HFL F 0

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

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

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_OMT_II	PS51683	SAM-dependent O-methyltransferase class II-type profile.	COMT1_MEDSA	24-363	3	A:24-362 C:24-363 F:24-363

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_OMT_II	PS51683	SAM-dependent O-methyltransferase class II-type profile.	COMT1_MEDSA	24-363	2	A:24-362 - F:24-363

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_OMT_II	PS51683	SAM-dependent O-methyltransferase class II-type profile.	COMT1_MEDSA	24-363	2	- C:24-363 -

(no "Exon" information available for 1KYW)

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:350
 aligned with COMT1_MEDSA | P28002 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:350
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
          COMT1_MEDSA    13 HISDEEANLFAMQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRLLACYIILTCSVRTQQDGKVQRLYGLATVAKYLVKNEDGVSISALNLMNQDKVLMESWYHLKDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYTGFEGLKSLVDVGGGTGAVINTIVSKYPTIKGINFDLPHVIEDAPSYPGVEHVGGDMFVSIPKADAVFMKWICHDWSDEHCLKFLKNCYEALPDNGKVIVAECILPVAPDSSLATKGVVHIDVIMLAHNPGGKERTQKEFEDLAKGAGFQGFKVHCNAFNTYIMEFL 362
               SCOP domains d1kywa1 A:13-119 Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase                                d1kywa2 A:120-362 Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase                                                                                                                                                                        SCOP domains
               CATH domains 1kywA01 A:13-115 'winged helix' repressor DNA binding domain                                           1kywA02 A:116-362 Vaccinia Virus protein VP39                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......hhhhhhh.......hhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeehhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeee.....hhhhhhhhhh...eeeeeehhhhhh.......eeeee............ee...hhhhhhhhhhhhhhhhhhhhh.....eeeee.........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh....eeeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------SAM_OMT_II  PDB: A:24-362 UniProt: 24-363                                                                                                                                                                                                                                                                                                           PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kyw A  13 HISDEEANLFAMQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRLLACYIILTCSVRTQQDGKVQRLYGLATVAKYLVKNEDGVSISALNLMNQDKVLMESWYHLKDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYTGFEGLKSLVDVGGGTGAVINTIVSKYPTIKGINFDLPHVIEDAPSYPGVEHVGGDMFVSIPKADAVFMKWICHDWSDEHCLKFLKNCYEALPDNGKVIVAECILPVAPDSSLATKGVVHIDVIMLAHNPGGKERTQKEFEDLAKGAGFQGFKVHCNAFNTYIMEFL 362
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362

Chain C from PDB  Type:PROTEIN  Length:361
 aligned with COMT1_MEDSA | P28002 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:361
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364 
          COMT1_MEDSA     5 GETQITPTHISDEEANLFAMQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRLLACYIILTCSVRTQQDGKVQRLYGLATVAKYLVKNEDGVSISALNLMNQDKVLMESWYHLKDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYTGFEGLKSLVDVGGGTGAVINTIVSKYPTIKGINFDLPHVIEDAPSYPGVEHVGGDMFVSIPKADAVFMKWICHDWSDEHCLKFLKNCYEALPDNGKVIVAECILPVAPDSSLATKGVVHIDVIMLAHNPGGKERTQKEFEDLAKGAGFQGFKVHCNAFNTYIMEFLKKV 365
               SCOP domains d1kywc1 C:5-119 Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase                                         d1kywc2 C:120-365 Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase                                                                                                                                                                           SCOP domains
               CATH domains 1kywC01 C:5-115 'winged helix' repressor DNA binding domain                                                    1kywC02 C:116-365 Vaccinia Virus protein VP39                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......hhhhhhh.......hhhhhhhhhhhhhhhh..eeeeeee.....eeeeeee.hhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee...................eeeeehhhhhh.......eeeee...........eee...hhhhhhhhhhhhhhhhhhhhh....eeeeeeeee......hhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhh....eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------SAM_OMT_II  PDB: C:24-363 UniProt: 24-363                                                                                                                                                                                                                                                                                                           -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kyw C   5 GETQITPTHISDEEANLFAMQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRLLACYIILTCSVRTQQDGKVQRLYGLATVAKYLVKNEDGVSISALNLMNQDKVLMESWYHLKDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYTGFEGLKSLVDVGGGTGAVINTIVSKYPTIKGINFDLPHVIEDAPSYPGVEHVGGDMFVSIPKADAVFMKWICHDWSDEHCLKFLKNCYEALPDNGKVIVAECILPVAPDSSLATKGVVHIDVIMLAHNPGGKERTQKEFEDLAKGAGFQGFKVHCNAFNTYIMEFLKKV 365
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364

Chain F from PDB  Type:PROTEIN  Length:361
 aligned with COMT1_MEDSA | P28002 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:361
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364 
          COMT1_MEDSA     5 GETQITPTHISDEEANLFAMQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRLLACYIILTCSVRTQQDGKVQRLYGLATVAKYLVKNEDGVSISALNLMNQDKVLMESWYHLKDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYTGFEGLKSLVDVGGGTGAVINTIVSKYPTIKGINFDLPHVIEDAPSYPGVEHVGGDMFVSIPKADAVFMKWICHDWSDEHCLKFLKNCYEALPDNGKVIVAECILPVAPDSSLATKGVVHIDVIMLAHNPGGKERTQKEFEDLAKGAGFQGFKVHCNAFNTYIMEFLKKV 365
               SCOP domains d1kywf1 F:5-119 Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase                                         d1kywf2 F:120-365 Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase                                                                                                                                                                           SCOP domains
               CATH domains 1kywF01 F:5-115 'winged helix' repressor DNA binding domain                                                    1kywF02 F:116-365 Vaccinia Virus protein VP39                                                                                                                                                                                                              CATH domains
           Pfam domains (1) -----------------------------Dimerisation-1kywF01 F:34-85                        ----------Methyltransf_2-1kywF04 F:96-340                                                                                                                                                                                                                      ------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------Dimerisation-1kywF02 F:34-85                        ----------Methyltransf_2-1kywF05 F:96-340                                                                                                                                                                                                                      ------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------Dimerisation-1kywF03 F:34-85                        ----------Methyltransf_2-1kywF06 F:96-340                                                                                                                                                                                                                      ------------------------- Pfam domains (3)
         Sec.struct. author ..........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......hhhhhhh.......hhhhhhhhhhhhhhhh..eeeeeee.....eeeeeee.hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhh...eeeeeehhhhhh.......eeeee...........eee...hhhhhhhhhhhhhhhhhhhh.....eeeeee.........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh...eeeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------SAM_OMT_II  PDB: F:24-363 UniProt: 24-363                                                                                                                                                                                                                                                                                                           -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kyw F   5 GETQITPTHISDEEANLFAMQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRLLACYIILTCSVRTQQDGKVQRLYGLATVAKYLVKNEDGVSISALNLMNQDKVLMESWYHLKDAVLDGGIPFNKAYGMTAFEYHGTDPRFNKVFNKGMSDHSTITMKKILETYTGFEGLKSLVDVGGGTGAVINTIVSKYPTIKGINFDLPHVIEDAPSYPGVEHVGGDMFVSIPKADAVFMKWICHDWSDEHCLKFLKNCYEALPDNGKVIVAECILPVAPDSSLATKGVVHIDVIMLAHNPGGKERTQKEFEDLAKGAGFQGFKVHCNAFNTYIMEFLKKV 365
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364

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(

)

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)

Medicago sativa. Organism_taxid: 3879. (5)

1a	1kywA02	A:116-362
1b	1kywC02	C:116-365
1c	1kywF02	F:116-365

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

Medicago sativa. Organism_taxid: 3879. (5)

2a	1kywA01	A:13-115
2b	1kywC01	C:5-115
2c	1kywF01	F:5-115

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Dimerisation (6)

Medicago sativa (Alfalfa) (2)

1a	Dimerisation-1kywF01	F:34-85
1b	Dimerisation-1kywF02	F:34-85
1c	Dimerisation-1kywF03	F:34-85

Clan: NADP_Rossmann (1239)

Family: Methyltransf_2 (13)

Medicago sativa (Alfalfa) (2)

2a	Methyltransf_2-1kywF04	F:96-340
2b	Methyltransf_2-1kywF05	F:96-340
2c	Methyltransf_2-1kywF06	F:96-340

Asymmetric Unit(hide GO term definitions)

Chain A,C,F (COMT1_MEDSA | P28002)

molecular function
	GO:0008171	O-methyltransferase activity	Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
	GO:0047763	caffeate O-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + 3,4-dihydroxy-trans-cinnamate = S-adenosyl-L-homocysteine + 3-methoxy-4-hydroxy-trans-cinnamate.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	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:0009809	lignin biosynthetic process	The chemical reactions and pathways resulting in the formation of lignins, a class of polymers formed by the dehydrogenetive radical polymerization of various phenylpropanoid monomers.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0009699	phenylpropanoid biosynthetic process	The chemical reactions and pathways resulting in the formation of aromatic derivatives of trans-cinnamic acid.

Asymmetric Unit
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	COMT1_MEDSA \| P28002	:	1kyz

1kyz	1KYZ IS THE CRYSTAL STRUCTURE ANALYSIS OF CAFFEIC ACID/5- HYDROXYFERULIC ACID 3/5-O-METHYLTRANSFERASE FERULIC ACID COMPLEX.

Description

Compounds

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Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

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