1BHM | PDE020 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA

Authors :   A. K. Aggarwal, M. Newman

Date :   12 Jul 95 (Deposition) - 12 Jul 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Hydrolase, Complex (Endonuclease/Dna), Nuclease, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Newman, T. Strzelecka, L. F. Dorner, I. Schildkraut, A. K. Aggarwal
Structure Of Bam Hi Endonuclease Bound To Dna: Partial Folding And Unfolding On Dna Binding.
Science V. 269 656 1995
PubMed-ID: 7624794
(for further references see the PDB file header)

*Molecule 1 - DNA (5'-D(TPAPTPGPGPAPTPCPCPAPTPA)- 3')*
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - PROTEIN (BAMHI (E.C.3.1.21.4))
	Chains	:	A, B
	EC Number	:	3.1.21.4
	Engineered	:	YES
	Organism Scientific	:	BACILLUS AMYLOLIQUEFACIENS
	Organism Taxid	:	1390
	Synonym	:	R. BAMHI

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1BHM)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	CTA	UNKNOWN	ASP A:94 , GLU A:111 , GLU A:113	NULL
2	CTB	UNKNOWN	ASP A:94 , GLU A:111 , GLU A:113	NULL

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

Asymmetric/Biological Unit

No.	Residues
1	Trp A:38	-	Pro A:39
2	Trp B:38	-	Pro B:39

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

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

(no "Exon" information available for 1BHM)

Asymmetric/Biological 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:198
 aligned with T2BA_BACAM | P23940 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:198
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        
           T2BA_BACAM     1 MEVEKEFITDEAKELLSKDKLIQQAYNEVKTSICSPIWPATSKTFTINNTEKNCNGVVPIKELCYTLLEDTYNWYREKPLDILKLEKKKGGPIDVYKEFIENSELKRVGMEFETGNISSAHRSMNKLLLGLKHGEIDLAIILMPIKQLAYYLTDRVTNFEELEPYFELTEGQPFIFIGFNAEAYNSNVPLIPKGSDGM 198
               SCOP domains d1bhma_ A: Restriction endonuclease BamHI                                                                                                                                                              SCOP domains
               CATH domains 1bhmA00 A:1-198  [code=3.40.91.20, no name defined]                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) .------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeee..eeeeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee.hhhh.........hhhhhhhhhhh....eeeeeee..eee............. Sec.struct. author (1)
     Sec.struct. author (2) -eeeeeee-------------------------------------eee--------------------------ee-------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1bhm A   1 MEVEKEFITDEAKELLSKDKLIQQAYNEVKTSICSPIWPATSKTFTINNTEKNCNGVVPIKELCYTLLEDTYNWYREKPLDILKLEKKKGGPIDVYKEFIENSELKRVGMEFETGNISSAHRSMNKLLLGLKHGEIDLAIILMPIKQLAYYLTDRVTNFEELEPYFELTEGQPFIFIGFNAEAYNSNVPLIPKGSDGM 198
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:208
 aligned with T2BA_BACAM | P23940 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
           T2BA_BACAM     1 MEVEKEFITDEAKELLSKDKLIQQAYNEVKTSICSPIWPATSKTFTINNTEKNCNGVVPIKELCYTLLEDTYNWYREKPLDILKLEKKKGGPIDVYKEFIENSELKRVGMEFETGNISSAHRSMNKLLLGLKHGEIDLAIILMPIKQLAYYLTDRVTNFEELEPYFELTEGQPFIFIGFNAEAYNSNVPLIPKGSDGMSKRSIKKWKD 208
               SCOP domains d1bhmb_ B: Restriction endonuclease BamHI                                                                                                                                                                        SCOP domains
               CATH domains 1bhmB00 B:1-208  [code=3.40.91.20, no name defined]                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeee..eeeeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee.hhhh.........hhhhhhhhhhh....eeeeeee..eee....................... Sec.struct. author (1)
     Sec.struct. author (2) -eeeeeee-------------------------------------eee--------------------------ee------------------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bhm B   1 MEVEKEFITDEAKELLSKDKLIQQAYNEVKTSICSPIWPATSKTFTINNTEKNCNGVVPIKELCYTLLEDTYNWYREKPLDILKLEKKKGGPIDVYKEFIENSELKRVGMEFETGNISSAHRSMNKLLLGLKHGEIDLAIILMPIKQLAYYLTDRVTNFEELEPYFELTEGQPFIFIGFNAEAYNSNVPLIPKGSDGMSKRSIKKWKD 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain C from PDB  Type:DNA  Length:12
                                            
                 1bhm C   1 TATGGATCCATA  12
                                    10

Chain D from PDB  Type:DNA  Length:11
                                           
                 1bhm D   1 TATGGATCCAT  11
                                    10

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Restriction endonuclease-like (209)

Superfamily: Restriction endonuclease-like (170)

Family: Restriction endonuclease BamHI (5)

Protein domain: Restriction endonuclease BamHI (5)

Bacillus amyloliquefaciens [TaxId: 1390] (5)

1a	d1bhma_	A:
1b	d1bhmb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Restriction Endonuclease (20)

Homologous Superfamily: [code=3.40.91.20, no name defined] (11)

[unclassified] (8)

1a	1bhmB00	B:1-208
1b	1bhmA00	A:1-198

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (T2BA_BACAM | P23940)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0009036	Type II site-specific deoxyribonuclease activity	Catalysis of the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates and 3' hydroxyls. Cleavage is dependent on the presence in the DNA of a specific recognition site; cleavage occurs at or very near this recognition site.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
	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:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1bhm)

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		CTA	[ RasMol ]	+environment [ RasMol ]
		CTB	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Trp A:38 - Pro A:39	[ RasMol ]
		Trp B:38 - Pro B:39	[ RasMol ]

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	1bhm
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	T2BA_BACAM \| P23940	:	1bam 1esg 2bam 3bam

(no "Related Entries Specified in the PDB File" available for 1BHM)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (1, 2)

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