1SUS - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ALFALFA FERUOYL COENZYME A 3-O-METHYLTRANSFERASE

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

Date :   26 Mar 04 (Deposition) - 15 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Rossmann Fold, Protein-Cofactor-Substrate Complex, O- Methyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. -L. Ferrer, C. Zubieta, R. A. Dixon, J. P. Noel
Crystal Structures Of Alfalfa Caffeoyl Coenzyme A 3-O-Methyltransferase
Plant Physiol. V. 137 1009 2005
PubMed-ID: 15734921 | Reference-DOI: 10.1104/PP.104.048751
(for further references see the PDB file header)

Molecule 1 - CAFFEOYL-COA O-METHYLTRANSFERASE
	Chains	:	A, B, C, D
	EC Number	:	2.1.1.104
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CCOMT
	Organism Scientific	:	MEDICAGO SATIVA
	Organism Taxid	:	3879
	Synonym	:	TRANS-CAFFEOYL-COA 3-O-METHYLTRANSFERASE, CCOAMT, CCOAOMT

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	SAH	4	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	SPF	1	Ligand/Ion	SINAPOYL COENZYME A

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	SPF	1	Ligand/Ion	SINAPOYL COENZYME A

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	SPF	-1	Ligand/Ion	SINAPOYL COENZYME A

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	SPF	-1	Ligand/Ion	SINAPOYL COENZYME A

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:63 , ASP A:163 , ASP A:189 , ASN A:190	BINDING SITE FOR RESIDUE CA A 305
2	AC2	SOFTWARE	ASP B:163 , LYS B:166 , ASN B:190 , HOH B:311	BINDING SITE FOR RESIDUE CA B 306
3	AC3	SOFTWARE	ASP C:163 , ASP C:189 , ASN C:190 , SAH C:303	BINDING SITE FOR RESIDUE CA C 307
4	AC4	SOFTWARE	MET D:61 , ASP D:163 , ASP D:189 , ASN D:190 , SAH D:304	BINDING SITE FOR RESIDUE CA D 308
5	AC5	SOFTWARE	MET A:61 , THR A:62 , THR A:63 , GLU A:85 , GLY A:87 , VAL A:88 , TYR A:89 , SER A:93 , ASP A:111 , ILE A:112 , PRO A:139 , ALA A:140 , ASP A:163 , ALA A:164 , ASP A:165 , TYR A:172 , SPF A:401 , HOH A:402 , PRO B:57 , HOH B:312	BINDING SITE FOR RESIDUE SAH A 301
6	AC6	SOFTWARE	THR B:62 , GLY B:87 , VAL B:88 , TYR B:89 , SER B:93 , ASP B:111 , ILE B:112 , ASP B:163 , ASP B:165 , TYR B:172 , HOH B:308	BINDING SITE FOR RESIDUE SAH B 302
7	AC7	SOFTWARE	MET C:61 , GLY C:87 , SER C:93 , ILE C:112 , ASN C:113 , PHE C:161 , ASP C:163 , ASP C:165 , CA C:307 , HOH C:313 , LYS D:207	BINDING SITE FOR RESIDUE SAH C 303
8	AC8	SOFTWARE	PRO C:57 , MET D:61 , THR D:62 , THR D:63 , VAL D:88 , SER D:93 , ASP D:111 , ILE D:112 , ALA D:140 , ASP D:163 , ALA D:164 , ASP D:165 , TYR D:172 , CA D:308	BINDING SITE FOR RESIDUE SAH D 304
9	AC9	SOFTWARE	LYS A:21 , ILE A:60 , ASP A:163 , ALA A:164 , ASP A:165 , LYS A:166 , TRP A:193 , ASN A:194 , PRO A:204 , TYR A:212 , SAH A:301 , TRP B:58 , HOH B:312	BINDING SITE FOR RESIDUE SPF A 401

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

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_OMT_I	PS51682	SAM-dependent O-methyltransferase class I-type profile.	CAMT_MEDSA	22-246	4	A:22-246 B:22-246 C:22-246 D:22-246

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_OMT_I	PS51682	SAM-dependent O-methyltransferase class I-type profile.	CAMT_MEDSA	22-246	2	A:22-246 - C:22-246 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_OMT_I	PS51682	SAM-dependent O-methyltransferase class I-type profile.	CAMT_MEDSA	22-246	2	- B:22-246 - -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_OMT_I	PS51682	SAM-dependent O-methyltransferase class I-type profile.	CAMT_MEDSA	22-246	2	- - - D:22-246

(no "Exon" information available for 1SUS)

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:227
 aligned with CAMT_MEDSA | Q40313 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:227
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
           CAMT_MEDSA    21 KSLLQSDALYQYILETSVFPREHEAMKELREVTAKHPWNIMTTSADEGQFLSMLLKLINAKNTMEIGVYTGYSLLATALAIPEDGKILAMDINKENYELGLPVIKKAGVDHKIDFREGPALPVLDEMIKDEKNHGSYDFIFVDADKDNYLNYHKRLIDLVKVGGVIGYDNTLWNGSVVAPPDAPLRKYVRYYRDFVLELNKALAVDPRIEICMLPVGDGITICRRIK 247
               SCOP domains d1susa_ A: Caffeoyl-CoA O-methyltransferase                                                                                                                                                                                         SCOP domains
               CATH domains 1susA00 A:21-247 Vaccinia Virus protein VP39                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhh.....eeee..hhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.....eee.....eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SAM_OMT_I  PDB: A:22-246 UniProt: 22-246                                                                                                                                                                                         - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sus A  21 KSLLQSDALYQYILETSVFPREHEAMKELREVTAKHPWNIMTTSADEGQFLSMLLKLINAKNTMEIGVYTGYSLLATALAIPEDGKILAMDINKENYELGLPVIKKAGVDHKIDFREGPALPVLDEMIKDEKNHGSYDFIFVDADKDNYLNYHKRLIDLVKVGGVIGYDNTLWNGSVVAPPDAPLRKYVRYYRDFVLELNKALAVDPRIEICMLPVGDGITICRRIK 247
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with CAMT_MEDSA | Q40313 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:227
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
           CAMT_MEDSA    21 KSLLQSDALYQYILETSVFPREHEAMKELREVTAKHPWNIMTTSADEGQFLSMLLKLINAKNTMEIGVYTGYSLLATALAIPEDGKILAMDINKENYELGLPVIKKAGVDHKIDFREGPALPVLDEMIKDEKNHGSYDFIFVDADKDNYLNYHKRLIDLVKVGGVIGYDNTLWNGSVVAPPDAPLRKYVRYYRDFVLELNKALAVDPRIEICMLPVGDGITICRRIK 247
               SCOP domains d1susb_ B: Caffeoyl-CoA O-methyltransferase                                                                                                                                                                                         SCOP domains
               CATH domains 1susB00 B:21-247 Vaccinia Virus protein VP39                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh....hhhhhhhhhhhhh........hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhh........eeeeee.....hhhhhhhhhhhheeeeeeeeee................hhhhhhhhhhhhhhhhhhhhh.....eee.....eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SAM_OMT_I  PDB: B:22-246 UniProt: 22-246                                                                                                                                                                                         - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sus B  21 KSLLQSDALYQYILETSVFPREHEAMKELREVTAKHPWNIMTTSADEGQFLSMLLKLINAKNTMEIGVYTGYSLLATALAIPEDGKILAMDINKENYELGLPVIKKAGVDHKIDFREGPALPVLDEMIKDEKNHGSYDFIFVDADKDNYLNYHKRLIDLVKVGGVIGYDNTLWNGSVVAPPDAPLRKYVRYYRDFVLELNKALAVDPRIEICMLPVGDGITICRRIK 247
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain C from PDB  Type:PROTEIN  Length:227
 aligned with CAMT_MEDSA | Q40313 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:227
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
           CAMT_MEDSA    21 KSLLQSDALYQYILETSVFPREHEAMKELREVTAKHPWNIMTTSADEGQFLSMLLKLINAKNTMEIGVYTGYSLLATALAIPEDGKILAMDINKENYELGLPVIKKAGVDHKIDFREGPALPVLDEMIKDEKNHGSYDFIFVDADKDNYLNYHKRLIDLVKVGGVIGYDNTLWNGSVVAPPDAPLRKYVRYYRDFVLELNKALAVDPRIEICMLPVGDGITICRRIK 247
               SCOP domains d1susc_ C: Caffeoyl-CoA O-methyltransferase                                                                                                                                                                                         SCOP domains
               CATH domains 1susC00 C:21-247 Vaccinia Virus protein VP39                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh......hhhhhhhhh............hhhhhhhhhhhhh...eeeee....hhhhhhhhhhh....eeeeee...hhhhhhhhhhhhh.hhhhh......hhhhhhhhhhh........eeee.....hhhhhhhhhhhhh.....eeee................hhhhhhhhhhhhhhhhhhhhh.....eee.....eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SAM_OMT_I  PDB: C:22-246 UniProt: 22-246                                                                                                                                                                                         - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sus C  21 KSLLQSDALYQYILETSVFPREHEAMKELREVTAKHPWNIMTTSADEGQFLSMLLKLINAKNTMEIGVYTGYSLLATALAIPEDGKILAMDINKENYELGLPVIKKAGVDHKIDFREGPALPVLDEMIKDEKNHGSYDFIFVDADKDNYLNYHKRLIDLVKVGGVIGYDNTLWNGSVVAPPDAPLRKYVRYYRDFVLELNKALAVDPRIEICMLPVGDGITICRRIK 247
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain D from PDB  Type:PROTEIN  Length:227
 aligned with CAMT_MEDSA | Q40313 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:227
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
           CAMT_MEDSA    21 KSLLQSDALYQYILETSVFPREHEAMKELREVTAKHPWNIMTTSADEGQFLSMLLKLINAKNTMEIGVYTGYSLLATALAIPEDGKILAMDINKENYELGLPVIKKAGVDHKIDFREGPALPVLDEMIKDEKNHGSYDFIFVDADKDNYLNYHKRLIDLVKVGGVIGYDNTLWNGSVVAPPDAPLRKYVRYYRDFVLELNKALAVDPRIEICMLPVGDGITICRRIK 247
               SCOP domains d1susd_ D: Caffeoyl-CoA O-methyltransferase                                                                                                                                                                                         SCOP domains
               CATH domains 1susD00 D:21-247 Vaccinia Virus protein VP39                                                                                                                                                                                        CATH domains
           Pfam domains (1) -------------Methyltransf_3-1susD01 D:34-246                                                                                                                                                                                      - Pfam domains (1)
           Pfam domains (2) -------------Methyltransf_3-1susD02 D:34-246                                                                                                                                                                                      - Pfam domains (2)
           Pfam domains (3) -------------Methyltransf_3-1susD03 D:34-246                                                                                                                                                                                      - Pfam domains (3)
           Pfam domains (4) -------------Methyltransf_3-1susD04 D:34-246                                                                                                                                                                                      - Pfam domains (4)
         Sec.struct. author .......hhhhhhhhh.......hhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhh.......ee..hhhhhhhhhhhhhh..............hhhhhhhhhh........eeee.....hhhhhh..hhhhhh.....eee................hhhhhhhhhhhhhhhhhhh........ee.....eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SAM_OMT_I  PDB: D:22-246 UniProt: 22-246                                                                                                                                                                                         - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sus D  21 KSLLQSDALYQYILETSVFPREHEAMKELREVTAKHPWNIMTTSADEGQFLSMLLKLINAKNTMEIGVYTGYSLLATALAIPEDGKILAMDINKENYELGLPVIKKAGVDHKIDFREGPALPVLDEMIKDEKNHGSYDFIFVDADKDNYLNYHKRLIDLVKVGGVIGYDNTLWNGSVVAPPDAPLRKYVRYYRDFVLELNKALAVDPRIEICMLPVGDGITICRRIK 247
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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(

)

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: COMT-like (31)

Protein domain: Caffeoyl-CoA O-methyltransferase (2)

Alfalfa (Medicago sativa) [TaxId: 3879] (2)

1a	d1susa_	A:
1b	d1susb_	B:
1c	d1susc_	C:
1d	d1susd_	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)

Medicago sativa. Organism_taxid: 3879. (2)

1a	1susA00	A:21-247
1b	1susB00	B:21-247
1c	1susC00	C:21-247
1d	1susD00	D:21-247

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: Methyltransf_3 (13)

Medicago sativa (Alfalfa) (2)

1a	Methyltransf_3-1susD01	D:34-246
1b	Methyltransf_3-1susD02	D:34-246
1c	Methyltransf_3-1susD03	D:34-246
1d	Methyltransf_3-1susD04	D:34-246

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CAMT_MEDSA | Q40313)

molecular function
	GO:0008171	O-methyltransferase activity	Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
	GO:0042409	caffeoyl-CoA O-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + caffeoyl-CoA = S-adenosyl-L-homocysteine + feruloyl-CoA.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor 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: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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	Cis Peptide Bonds
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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