1SVU - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE Q237W MUTANT OF HHAI DNA METHYLTRANSFERASE: AN INSIGHT INTO PROTEIN-PROTEIN INTERACTIONS

Authors :   A. Dong, L. Zhou, X. Zhang, S. Stickel, R. J. Roberts, X. Cheng

Date :   30 Mar 04 (Deposition) - 29 Jun 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.66

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

Keywords :   Dna Methyltransferase, Protein-Protein Interactions, Evolutionary Link, Type I And Ii Restriction-Modification Systems (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Dong, L. Zhou, X. Zhang, S. Stickel, R. J. Roberts, X. Cheng
Structure Of The Q237W Mutant Of Hhai Dna Methyltransferase: An Insight Into Protein-Protein Interactions
Biol. Chem. V. 385 373 2004
PubMed-ID: 15195996 | Reference-DOI: 10.1515/BCHM.385.13.373.57208
(for further references see the PDB file header)

Molecule 1 - MODIFICATION METHYLASE HHAI
	Chains	:	A, B
	EC Number	:	2.1.1.37
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	HHAIM
	Mutation	:	YES
	Organism Scientific	:	HAEMOPHILUS HAEMOLYTICUS
	Organism Taxid	:	726
	Synonym	:	CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI, M.HHAI

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 21)

No.	Name	Count	Type	Full Name
1	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	SO4	2	Ligand/Ion	SULFATE ION
3	UNX	17	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (3, 11)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	SO4	2	Ligand/Ion	SULFATE ION
3	UNX	8	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 2 (2, 10)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	SO4	-1	Ligand/Ion	SULFATE ION
3	UNX	9	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:13 , PRO A:70 , ASP A:71 , LYS A:114 , ARG A:172	BINDING SITE FOR RESIDUE SO4 A 600
02	AC2	SOFTWARE	THR A:226 , ARG A:228 , TYR A:242	BINDING SITE FOR RESIDUE SO4 A 601
03	AC3	SOFTWARE	PHE A:18 , ALA A:19 , GLY A:20 , LEU A:21 , GLY A:22 , GLY A:23 , ASN A:39 , GLU A:40 , TRP A:41 , ASP A:60 , ILE A:61 , THR A:62 , GLY A:78 , LEU A:100 , TYR A:285 , ASN A:304 , SER A:305	BINDING SITE FOR RESIDUE SAH A 401
04	AC4	SOFTWARE	PHE B:18 , ALA B:19 , GLY B:20 , LEU B:21 , GLY B:23 , ASN B:39 , GLU B:40 , TRP B:41 , GLY B:59 , ASP B:60 , ILE B:61 , LEU B:100 , SER B:305 , VAL B:306	BINDING SITE FOR RESIDUE SAH B 402
05	AC5	SOFTWARE	LYS B:43 , GLU B:47	BINDING SITE FOR RESIDUE UNX B 404
06	AC6	SOFTWARE	VAL B:291	BINDING SITE FOR RESIDUE UNX B 405
07	AC7	SOFTWARE	ARG A:240	BINDING SITE FOR RESIDUE UNX A 602
08	AC8	SOFTWARE	TYR A:254	BINDING SITE FOR RESIDUE UNX A 603
09	AC9	SOFTWARE	ASP B:60	BINDING SITE FOR RESIDUE UNX B 406
10	BC1	SOFTWARE	LYS A:210	BINDING SITE FOR RESIDUE UNX B 407
11	BC2	SOFTWARE	LYS A:67	BINDING SITE FOR RESIDUE UNX A 604
12	BC3	SOFTWARE	ASN A:52	BINDING SITE FOR RESIDUE UNX A 605
13	BC4	SOFTWARE	GLU B:203	BINDING SITE FOR RESIDUE UNX B 410
14	BC5	SOFTWARE	PRO B:198	BINDING SITE FOR RESIDUE UNX B 411

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

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

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_C5	PS51679	C-5 cytosine-specific DNA methylase (Dnmt) domain profile.	MTH1_HAEPH	12-325	2	A:12-325 B:12-325
2	C5_MTASE_1	PS00094	C-5 cytosine-specific DNA methylases active site.	MTH1_HAEPH	73-85	2	A:73-79 B:73-83
3	C5_MTASE_2	PS00095	C-5 cytosine-specific DNA methylases C-terminal signature.	MTH1_HAEPH	300-318	2	A:300-318 B:300-318

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_C5	PS51679	C-5 cytosine-specific DNA methylase (Dnmt) domain profile.	MTH1_HAEPH	12-325	1	A:12-325 -
2	C5_MTASE_1	PS00094	C-5 cytosine-specific DNA methylases active site.	MTH1_HAEPH	73-85	1	A:73-79 -
3	C5_MTASE_2	PS00095	C-5 cytosine-specific DNA methylases C-terminal signature.	MTH1_HAEPH	300-318	1	A:300-318 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_C5	PS51679	C-5 cytosine-specific DNA methylase (Dnmt) domain profile.	MTH1_HAEPH	12-325	1	- B:12-325
2	C5_MTASE_1	PS00094	C-5 cytosine-specific DNA methylases active site.	MTH1_HAEPH	73-85	1	- B:73-83
3	C5_MTASE_2	PS00095	C-5 cytosine-specific DNA methylases C-terminal signature.	MTH1_HAEPH	300-318	1	- B:300-318

(no "Exon" information available for 1SVU)

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:307
 aligned with MTH1_HAEPH | P05102 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:327
                                    10        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       
           MTH1_HAEPH     1 MIEIKDKQLTGLRFIDLFAGLGGFRLALESCGAECVYSNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDHDILCAGFPCQAFSISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRERIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDSEVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGKGGQGERIYSTRGIAITLSAYGGGIFAKTGGYLVNGKTRKLHPRECARVMGYPDSYKVHPSTSQAYKQFGNSVVINVLQYIAYNIGSSLNFKPY 327
               SCOP domains d1svua_ A: DNA methylase HhaI                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1svuA01 A:1-186,A:285-327 Vaccinia Virus protein VP39                                                                                                                                     1svuA02 A:187-284 DNA Methylase, subunit A, domain 2                                              1svuA01 A:1-186,A:285-327                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee....hhhhhhhhhh..eeeee...hhhhhhhhhhhhh.....hhhhh.........eeee..--------------------hhhhhhhhhhhh...eeeeeee.hhh.hhhhhhhhhhhhhhhh...eeeeeeee.hhhh..ee.eeeeeeee.hhhh..............hhhhhh.hhhhhhhhh.....ee................eee.......eee.....ee..............eee....eee.hhhhhhhhh..........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------SAM_MT_C5  PDB: A:12-325 UniProt: 12-325                                                                                                                                                                                                                                                                                  -- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------C5_MTASE_1   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C5_MTASE_2         --------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1svu A   1 MIEIKDKQLTGLRFIDLFAGLGGFRLALESCGAECVYSNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDHDILCAGF--------------------LFFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRERIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDSEVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGKGGWGERIYSTRGIAITLSAYGGGIFAKTGGYLVNGKTRKLHPRECARVMGYPDSYKVHPSTSQAYKQFGNSVVINVLQYIAYNIGSSLNFKPY 327
                                    10        20        30        40        50        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       
                                                                                                         79                  100

Chain B from PDB  Type:PROTEIN  Length:314
 aligned with MTH1_HAEPH | P05102 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:327
                                    10        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       
           MTH1_HAEPH     1 MIEIKDKQLTGLRFIDLFAGLGGFRLALESCGAECVYSNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDHDILCAGFPCQAFSISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRERIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDSEVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGKGGQGERIYSTRGIAITLSAYGGGIFAKTGGYLVNGKTRKLHPRECARVMGYPDSYKVHPSTSQAYKQFGNSVVINVLQYIAYNIGSSLNFKPY 327
               SCOP domains d1svub_ B: DNA methylase HhaI                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1svuB01 B:1-186,B:285-327 Vaccinia Virus protein VP39                                                                                                                                     1svuB02 B:187-284 DNA Methylase, subunit A, domain 2                                              1svuB01 B:1-186,B:285-327                   CATH domains
           Pfam domains (1) -----------DNA_methylase-1svuB01 B:12-320                                                                                                                                                                                                                                                                                       ------- Pfam domains (1)
           Pfam domains (2) -----------DNA_methylase-1svuB02 B:12-320                                                                                                                                                                                                                                                                                       ------- Pfam domains (2)
         Sec.struct. author ............eeeee....hhhhhhhhhhh.eeeeee..hhhhhhhhhhhhh..........hhhhh....eeeee.....-------------......hhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhhhh....eeeeee.hhh......eeeeeeee...................hhhhhh.hhhhhhh.ee....................eeee........eee.....................eeee..eee..hhhhhhhhh..........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------SAM_MT_C5  PDB: B:12-325 UniProt: 12-325                                                                                                                                                                                                                                                                                  -- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------C5_MTASE_1   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C5_MTASE_2         --------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1svu B   1 MIEIKDKQLTGLRFIDLFAGLGGFRLALESCGAECVYSNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDHDILCAGFPCQA-------------RGTLFFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIPQKRERIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDSEVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGKGGWGERIYSTRGIAITLSAYGGGIFAKTGGYLVNGKTRKLHPRECARVMGYPDSYKVHPSTSQAYKQFGNSVVINVLQYIAYNIGSSLNFKPY 327
                                    10        20        30        40        50        60        70        80  |      -      |100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       
                                                                                                             83            97

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	-	→ 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)

Haemophilus haemolyticus. Organism_taxid: 726. (1)

1a	1svuB01	B:1-186,B:285-327
1b	1svuA01	A:1-186,A:285-327

Architecture: Alpha-Beta Complex (3881)

Topology: DNA Methylase; Chain A, domain 2 (31)

Homologous Superfamily: DNA Methylase, subunit A, domain 2 (31)

Haemophilus haemolyticus. Organism_taxid: 726. (1)

2a	1svuA02	A:187-284
2b	1svuB02	B:187-284

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: DNA_methylase (15)

Haemophilus parahaemolyticus (11)

1a	DNA_methylase-1svuB01	B:12-320
1b	DNA_methylase-1svuB02	B:12-320

Asymmetric Unit(hide GO term definitions)

Chain A,B (MTH1_HAEPH | P05102)

molecular function
	GO:0003886	DNA (cytosine-5-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + DNA containing cytosine = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine.
	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:0090116	C-5 methylation of cytosine	The covalent transfer of a methyl group to C-5 of cytosine in a DNA molecule.
	GO:0009307	DNA restriction-modification system	A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.

Asymmetric Unit
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1mht	M.HHAI-ADOHCY-DNA COMPLEX IN R32 SPACE GROUP
2hmy	M.HHAI-ADOMET IN P21 SPACE GROUP

Description

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Ligands, Modified Residues, Ions (3, 21)

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