1LT7 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   OXIDIZED HOMO SAPIENS BETAINE-HOMOCYSTEINE S-METHYLTRANSFERASE IN COMPLEX WITH FOUR SM(III) IONS

Authors :   J. C. Evans, D. P. Huddler, J. Jiracek, C. Castro, N. S. Millian, T. A. Gar M. L. Ludwig

Date :   20 May 02 (Deposition) - 11 Sep 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Transferase, Homocysteine Metabolism, Homocysteinemia, Thiol Alkyl Transfer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. C. Evans, D. P. Huddler, J. Jiracek, C. Castro, N. S. Millian, T. A. Garrow, M. L. Ludwig
Betaine-Homocysteine Methyltransferase: Zinc In A Distorted Barrel.
Structure V. 10 1159 2002
PubMed-ID: 12220488 | Reference-DOI: 10.1016/S0969-2126(02)00796-7

Molecule 1 - BETAINE-HOMOCYSTEINE METHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PTYB4
	Expression System Strain	:	BL21-DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BETAINE-HOMOCYSTEINE S-METHYLTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	CIT	2	Ligand/Ion	CITRIC ACID
2	SM	4	Ligand/Ion	SAMARIUM (III) ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	CIT	4	Ligand/Ion	CITRIC ACID
2	SM	-1	Ligand/Ion	SAMARIUM (III) ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CIT	2	Ligand/Ion	CITRIC ACID
2	SM	-1	Ligand/Ion	SAMARIUM (III) ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CIT A:601 , HOH A:618 , HOH A:646	BINDING SITE FOR RESIDUE SM A 501
2	AC2	SOFTWARE	HOH A:694 , HOH B:702	BINDING SITE FOR RESIDUE SM B 502
3	AC3	SOFTWARE	HOH A:749	BINDING SITE FOR RESIDUE SM A 503
4	AC4	SOFTWARE	CIT B:602	BINDING SITE FOR RESIDUE SM B 504
5	AC5	SOFTWARE	HIS A:252 , LYS A:283 , ARG A:356 , SM A:501 , HOH A:615 , HOH A:641 , HOH A:646 , TYR B:363 , LYS B:369	BINDING SITE FOR RESIDUE CIT A 601
6	AC6	SOFTWARE	GLY A:360 , PRO A:362 , TYR A:363 , ASP B:220 , HIS B:252 , ARG B:356 , SM B:504 , HOH B:606 , HOH B:639	BINDING SITE FOR RESIDUE CIT B 602

Asymmetric Unit

No.	Residues
1	A:217	-	A:299
2	B:217	-	B:299

Asymmetric Unit

No.	Residues
1	Phe A:267	-	Pro A:268
2	Phe B:267	-	Pro B:268

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_061345	G	199	S	BHMT1_HUMAN	Polymorphism	59866108	A/B	G	199	S
2	UniProt	VAR_015886	R	239	Q	BHMT1_HUMAN	Polymorphism	3733890	A/B	Q	239	Q

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

Biological Unit 1 (2, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_061345	G	199	S	BHMT1_HUMAN	Polymorphism	59866108	A/B	G	199	S
2	UniProt	VAR_015886	R	239	Q	BHMT1_HUMAN	Polymorphism	3733890	A/B	Q	239	Q

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

Biological Unit 2 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_061345	G	199	S	BHMT1_HUMAN	Polymorphism	59866108	A/B	G	199	S
2	UniProt	VAR_015886	R	239	Q	BHMT1_HUMAN	Polymorphism	3733890	A/B	Q	239	Q

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HCY	PS50970	Homocysteine-binding domain profile.	BHMT1_HUMAN	11-314	2	A:11-314 B:11-314

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HCY	PS50970	Homocysteine-binding domain profile.	BHMT1_HUMAN	11-314	4	A:11-314 B:11-314

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HCY	PS50970	Homocysteine-binding domain profile.	BHMT1_HUMAN	11-314	2	A:11-314 B:11-314

Asymmetric Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000274353	1a	ENSE00001879035	chr5:78407602-78407741	140	BHMT1_HUMAN	1-11	11	2	A:11-11 B:11-11	1 1
1.2b	ENST00000274353	2b	ENSE00000971690	chr5:78411590-78411722	133	BHMT1_HUMAN	12-56	45	2	A:12-56 (gaps) B:12-56 (gaps)	45 45
1.3a	ENST00000274353	3a	ENSE00000971691	chr5:78415082-78415200	119	BHMT1_HUMAN	56-95	40	2	A:56-75 B:56-75	20 20
1.4a	ENST00000274353	4a	ENSE00000971692	chr5:78416173-78416364	192	BHMT1_HUMAN	96-159	64	2	A:99-159 B:99-159	61 61
1.5a	ENST00000274353	5a	ENSE00000971693	chr5:78417041-78417188	148	BHMT1_HUMAN	160-209	50	2	A:160-209 B:160-209	50 50
1.6a	ENST00000274353	6a	ENSE00000971694	chr5:78421869-78422051	183	BHMT1_HUMAN	209-270	62	2	A:209-270 B:209-270	62 62
1.7b	ENST00000274353	7b	ENSE00001787224	chr5:78423578-78423806	229	BHMT1_HUMAN	270-346	77	2	A:270-346 (gaps) B:270-346 (gaps)	77 77
1.8c	ENST00000274353	8c	ENSE00001953069	chr5:78426756-78428108	1353	BHMT1_HUMAN	346-406	61	2	A:346-371 B:346-371	26 26

Asymmetric Unit

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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:305
 aligned with BHMT1_HUMAN | Q93088 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:361
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370 
          BHMT1_HUMAN    11 KGILERLNAGEIVIGDGGFVFALEKRGYVKAGPWTPEAAVEHPEAVRQLHREFLRAGSNVMQTFTFYASEDKLENRGNYVLEKISGQEVNEAACDIARQVADEGDALVAGGVSQTPSYLSCKSETEVKKVFLQQLEVFMKKNVDFLIAEYFEHVEEAVWAVETLIASGKPVAATMCIGPEGDLHGVPPGECAVRLVKAGASIIGVNCHFDPTISLKTVKLMKEGLEAARLKAHLMSQPLAYHTPDCNKQGFIDLPEFPFGLEPRVATRWDIQKYAREAYNLGVRYIGGCCGFEPYHIRAIAEELAPERGFLPPASEKHGSWGSGLDMHTKPWVRARARKEYWENLRIASGRPYNPSMSKPD 371
               SCOP domains d1lt7a_ A: Betaine-homocyste             ine S-methyltransferase                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1lt7A00 A:11-371  [code=3.20             .20.330, no name defined                       ]                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...ee...hhhhhhhhhh.-------------hhhhhhhhhhhhhhhh..eeeee.-----------------------hhhhhhhhhhhhhhh...eeeeee..hhhhhh..hhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhh....eeeee............hhhhh......hhhhh.hhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhhhh....--------------------....hhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S---------------------------------------Q------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE HCY  PDB: A:11-314 UniProt: 11-314                                                                                                                                                                                                                                                                              --------------------------------------------------------- PROSITE
           Transcript 1 (1) 1Exon 1.2b  PDB: A:12-56 (gaps) UniProt: 12-56---------------------------------------Exon 1.4a  PDB: A:99-159 UniProt: 96-159 [INCOMPLETE]           Exon 1.5a  PDB: A:160-209 UniProt: 160-209        ------------------------------------------------------------Exon 1.7b  PDB: A:270-346 (gaps) UniProt: 270-346                            ------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3a  PDB: A:56-75 UniProt: 56-95  -----------------------------------------------------------------------------------------------------------------Exon 1.6a  PDB: A:209-270 UniProt: 209-270                    ---------------------------------------------------------------------------Exon 1.8c  PDB: A:346-371  Transcript 1 (2)
                 1lt7 A  11 KGILERLNAGEIVIGDGGFVFALEKRGY-------------HPEAVRQLHREFLRAGSNVMQTFT-----------------------VNEAAADIARQVADEGDALVAGGVSQTPSYLSAKSETEVKKVFLQQLEVFMKKNVDFLIAEYFEHVEEAVWAVETLIASGKPVAATMAIGPEGDLHGVPPGEAAVRLVKAGASIIGVNCHFDPTISLKTVKLMKEGLEAAQLKAHLMSQPLAYHTPDANKQGFIDLPEFPFGLEPRVATRWDIQKYAREAYNLGVRYIGGCCGFEPYHIRAIAEELAPERGFLPP--------------------RARARKEYWENLRIASGRPYNPSMSKPD 371
                                    20        30       | -         - |      60        70    |    -         -       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320  |      -         -   |   350       360       370 
                                                      38            52                     75                      99                                                                                                                                                                                                                             323                  344

Chain B from PDB  Type:PROTEIN  Length:315
 aligned with BHMT1_HUMAN | Q93088 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:361
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370 
          BHMT1_HUMAN    11 KGILERLNAGEIVIGDGGFVFALEKRGYVKAGPWTPEAAVEHPEAVRQLHREFLRAGSNVMQTFTFYASEDKLENRGNYVLEKISGQEVNEAACDIARQVADEGDALVAGGVSQTPSYLSCKSETEVKKVFLQQLEVFMKKNVDFLIAEYFEHVEEAVWAVETLIASGKPVAATMCIGPEGDLHGVPPGECAVRLVKAGASIIGVNCHFDPTISLKTVKLMKEGLEAARLKAHLMSQPLAYHTPDCNKQGFIDLPEFPFGLEPRVATRWDIQKYAREAYNLGVRYIGGCCGFEPYHIRAIAEELAPERGFLPPASEKHGSWGSGLDMHTKPWVRARARKEYWENLRIASGRPYNPSMSKPD 371
               SCOP domains d1lt7b_ B: Betaine-homocyste             ine S-methyltransferase                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1lt7B00 B:11-371  [code=3.20             .20.330, no name defined                       ]                                                                                                                                                                                                                                                                                 CATH domains
           Pfam domains (1) ------S-methyl_trans-1lt7B01              B:17-316                                                                                                                                                                                                                                                                -------          -------------------------------------- Pfam domains (1)
           Pfam domains (2) ------S-methyl_trans-1lt7B02              B:17-316                                                                                                                                                                                                                                                                -------          -------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhh...ee...hhhhhhhhh..-------------hhhhhhhhhhhhhhhh..eeeee.-----------------------hhhhhhhhhhhhhh....eeeeee..hhhhh....hhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhh....eeeee............hhhhh......hhhhh.hhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhhhh....----------hhhhh.hhhhhh..hhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S---------------------------------------Q------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE HCY  PDB: B:11-314 UniProt: 11-314                                                                                                                                                                                                                                                                              --------------------------------------------------------- PROSITE
           Transcript 1 (1) 1Exon 1.2b  PDB: B:12-56 (gaps) UniProt: 12-56---------------------------------------Exon 1.4a  PDB: B:99-159 UniProt: 96-159 [INCOMPLETE]           Exon 1.5a  PDB: B:160-209 UniProt: 160-209        ------------------------------------------------------------Exon 1.7b  PDB: B:270-346 (gaps) UniProt: 270-346                            ------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3a  PDB: B:56-75 UniProt: 56-95  -----------------------------------------------------------------------------------------------------------------Exon 1.6a  PDB: B:209-270 UniProt: 209-270                    ---------------------------------------------------------------------------Exon 1.8c  PDB: B:346-371  Transcript 1 (2)
                 1lt7 B  11 KGILERLNAGEIVIGDGGFVFALEKRGY-------------HPEAVRQLHREFLRAGSNVMQTFT-----------------------VNEAAADIARQVADEGDALVAGGVSQTPSYLSAKSETEVKKVFLQQLEVFMKKNVDFLIAEYFEHVEEAVWAVETLIASGKPVAATMAIGPEGDLHGVPPGEAAVRLVKAGASIIGVNCHFDPTISLKTVKLMKEGLEAAQLKAHLMSQPLAYHTPDANKQGFIDLPEFPFGLEPRVATRWDIQKYAREAYNLGVRYIGGCCGFEPYHIRAIAEELAPERGFLPP----------GLDMHTKPWVRARARKEYWENLRIASGRPYNPSMSKPD 371
                                    20        30       | -         - |      60        70    |    -         -       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320  |      -   |   340       350       360       370 
                                                      38            52                     75                      99                                                                                                                                                                                                                             323        334

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Homocysteine S-methyltransferase (11)

Family: Homocysteine S-methyltransferase (11)

Protein domain: Betaine-homocysteine S-methyltransferase (3)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d1lt7a_	A:
1b	d1lt7b_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: [code=3.20.20.330, no name defined] (11)

Human (Homo sapiens) (2)

1a	1lt7B00	B:11-371
1b	1lt7A00	A:11-371

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: S-methyl_trans] (7)

Family: S-methyl_trans (7)

Homo sapiens (Human) (2)

1a	S-methyl_trans-1lt7B01	B:17-316
1b	S-methyl_trans-1lt7B02	B:17-316

Asymmetric Unit(hide GO term definitions)

Chain A,B (BHMT1_HUMAN | Q93088)

molecular function
	GO:0008898	S-adenosylmethionine-homocysteine S-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + L-homocysteine = S-adenosyl-L-homocysteine + L-methionine.
	GO:0047150	betaine-homocysteine S-methyltransferase activity	Catalysis of the reaction: L-homocysteine + betaine = N,N-dimethylglycine + L-methionine.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0071267	L-methionine salvage	Any process that generates L-methionine from derivatives of it, without de novo synthesis.
	GO:0046500	S-adenosylmethionine metabolic process	The chemical reactions and pathways involving S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.
	GO:0006579	amino-acid betaine catabolic process	The chemical reactions and pathways resulting in the breakdown of any betaine, the N-trimethyl derivative of an amino acid.
	GO:0006577	amino-acid betaine metabolic process	The chemical reactions and pathways involving any betaine, the N-trimethyl derivative of an amino acid.
	GO:0042426	choline catabolic process	The chemical reactions and pathways resulting in the breakdown of choline (2-hydroxyethyltrimethylammonium), an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids and in the neurotransmitter acetylcholine.
	GO:0009086	methionine biosynthetic process	The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0006479	protein methylation	The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
	GO:0050666	regulation of homocysteine metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving homocysteine, the amino acid alpha-amino-gamma-mercaptobutanoic acid.
	GO:0000096	sulfur amino acid metabolic process	The chemical reactions and pathways involving amino acids containing sulfur, comprising cysteine, homocysteine, methionine and selenocysteine.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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	BHMT1_HUMAN \| Q93088	:	1lt8 4m3p

1lt8	1LT8 IS REDUCED HOMO SAPIENS BETAINE-HOMOCYSTEINE S- METHYLTRANSFERASE IN COMPLEX WITH S-(DELTA-CARBOXYBUTYL)-L- HOMOCYSTEINE

Description

Compounds

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Ligands, Modified Residues, Ions (2, 6)

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SS Bonds (2, 2)

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