1XHV | PD0595 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   HINCII BOUND TO CLEAVED COGNATE DNA GTCGAC AND MN2+

Authors :   C. Etzkorn, N. C. Horton

Date :   20 Sep 04 (Deposition) - 28 Sep 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,E,F,G,H  (1x)
Biol. Unit 2: C,D,I,J,K,L  (1x)

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

Reference :   C. Etzkorn, N. C. Horton
Mechanistic Insights From The Structures Of Hincii Bound To Cognate Dna Cleaved From Addition Of Mg(2+) And Mn(2+)
J. Mol. Biol. V. 343 833 2004
PubMed-ID: 15476804 | Reference-DOI: 10.1016/J.JMB.2004.08.082
(for further references see the PDB file header)

*Molecule 1 - 5'-D(GPCPCPGPGPTPC)-3'**
	Chains	:	E, G, I, K
	Engineered	:	YES
	Other Details	:	PHOSPHORAMIDITE SYNTHETIC CHEMISTRY
	Synthetic	:	YES

*Molecule 2 - 5'-D(PGPAPCPCPGPG)-3'*
	Chains	:	F, H, J, L
	Engineered	:	YES
	Other Details	:	PHOSPHORAMIDITE SYNTHETIC CHEMISTRY
	Synthetic	:	YES

Molecule 3 - TYPE II RESTRICTION ENZYME HINCII
	Chains	:	A, B, C, D
	EC Number	:	3.1.21.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	HINCIIR
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	727
	Synonym	:	ENDONUCLEASE HINCII, R.HINCII

		1	2	3	4	5	6	7	8	9	10	11	12
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J	K	L
Biological Unit 1 (1x)	:	A	B			E	F	G	H
Biological Unit 2 (1x)	:			C	D					I	J	K	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 22)

No.	Name	Count	Type	Full Name
1	MN	22	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (22, 22)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU B:38 , ASP B:114 , VAL B:128 , HOH B:1333 , DG F:8	BINDING SITE FOR RESIDUE MN B 1101
02	AC2	SOFTWARE	ASP B:114 , HOH B:1157 , HOH B:1158 , HOH B:1333 , DC E:7 , HOH E:1078 , DG F:8	BINDING SITE FOR RESIDUE MN F 1102
03	AC3	SOFTWARE	GLU A:38 , ASP A:114 , VAL A:128 , HOH A:1201 , DG H:8 , HOH H:968	BINDING SITE FOR RESIDUE MN A 1103
04	AC4	SOFTWARE	HIS A:73 , GLU A:74 , DG F:13 , HOH F:735 , HOH F:1322	BINDING SITE FOR RESIDUE MN A 1105
05	AC5	SOFTWARE	HIS D:73 , GLU D:74 , HOH D:1237 , HOH D:1267 , DG L:13	BINDING SITE FOR RESIDUE MN D 1106
06	AC6	SOFTWARE	HIS B:73 , GLU B:74 , LYS B:93 , HOH B:1296 , HOH B:1426 , ASP C:214 , DG H:13	BINDING SITE FOR RESIDUE MN B 1107
07	AC7	SOFTWARE	HOH J:716 , DG K:1 , HOH K:353	BINDING SITE FOR RESIDUE MN J 1108
08	AC8	SOFTWARE	ASP A:114 , ASP A:127 , HOH A:1128 , HOH A:1201 , HOH A:1224 , DC G:7 , DG H:8	BINDING SITE FOR RESIDUE MN H 1109
09	AC9	SOFTWARE	GLU D:38 , ASP D:114 , VAL D:128 , HOH D:1311 , DG J:8	BINDING SITE FOR RESIDUE MN D 1114
10	BC1	SOFTWARE	ASP D:114 , ASP D:127 , HOH D:1311 , DC I:7 , DG J:8	BINDING SITE FOR RESIDUE MN D 1115
11	BC2	SOFTWARE	HIS C:73 , GLU C:74 , HOH C:1162 , HOH C:1247 , DG J:13 , HOH J:247	BINDING SITE FOR RESIDUE MN C 1116
12	BC3	SOFTWARE	ASP C:114 , ASP C:127 , DC K:7 , DG L:8	BINDING SITE FOR RESIDUE MN C 1117
13	BC4	SOFTWARE	GLU C:38 , ASP C:114 , VAL C:128 , HOH C:1270 , DG L:8	BINDING SITE FOR RESIDUE MN C 1118
14	BC5	SOFTWARE	HOH F:1030 , HOH F:1031 , HOH F:1033 , DG G:1	BINDING SITE FOR RESIDUE MN G 1120
15	BC6	SOFTWARE	GLU B:35 , MN B:1128 , HOH B:1331 , HOH B:1332 , DG F:8	BINDING SITE FOR RESIDUE MN F 1121
16	BC7	SOFTWARE	GLU C:38 , DG L:8 , HOH L:1062 , MN L:1123	BINDING SITE FOR RESIDUE MN L 1122
17	BC8	SOFTWARE	DG L:8 , HOH L:990 , MN L:1122	BINDING SITE FOR RESIDUE MN L 1123
18	BC9	SOFTWARE	GLU D:38 , ASP D:114 , DG J:8 , HOH J:306	BINDING SITE FOR RESIDUE MN J 1124
19	CC1	SOFTWARE	HOH D:1303 , HOH D:1310 , DG J:8 , HOH J:309 , HOH J:996	BINDING SITE FOR RESIDUE MN J 1125
20	CC2	SOFTWARE	GLU A:38 , GLU A:107 , ASP A:114 , DG H:8 , HOH H:967	BINDING SITE FOR RESIDUE MN H 1126
21	CC3	SOFTWARE	GLY B:30 , DG H:8 , HOH H:1325	BINDING SITE FOR RESIDUE MN H 1127
22	CC4	SOFTWARE	HIS B:31 , GLN B:109 , HOH B:1422 , DG F:8 , MN F:1121	BINDING SITE FOR RESIDUE MN B 1128

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

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

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

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

(no "Exon" information available for 1XHV)

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:254
 aligned with T2C2_HAEIF | P17743 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
           T2C2_HAEIF     2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKRRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDSELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYIL 258
               SCOP domains d1xhva_ A: Restriction    endonuclease HincII                                                                                                                                                                                                                     SCOP domains
               CATH domains 1xhvA00 A:2-258  [code   =3.40.600.10, no name defined]                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eee..---...hhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh.....hhhhhhhh..hhhhhhhhh.hhhhhhh................eeeee..eeeeeeeeeee........eeeehhhhhhhhhhhhhhh....eeeeeeeeeeeee..eeeeeeeeeee.hhhhhhhh.ee.....eee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xhv A   2 SFIKPIYQDINSILIGQKVKRP---TLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYIL 258
                                    11        21 |   |  31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
                                                23  27

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with T2C2_HAEIF | P17743 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
           T2C2_HAEIF     2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKRRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDSELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
               SCOP domains d1xhvb_ B: Restriction e    ndonuclease HincII                                                                                                                                                                                                                   SCOP domains
               CATH domains 1xhvB00 B:2-257  [code=3    .40.600.10, no name defined]                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eee....----....hhhhhhhhhhhhhh.....eehhhhhhhhhhhh.....hhhhhhhh..hhhhhhhhh.hhhhhhh................eeeee..eeeeeeeeeee........eeeehhhhhhhhhhhhhhh....eeeeeeeeeeeee..eeeeeeeeeee.hhhhhhhh.ee.....eee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xhv B   2 SFIKPIYQDINSILIGQKVKRPKS----GHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
                                    11        21   |    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
                                                  25   30

Chain C from PDB  Type:PROTEIN  Length:247
 aligned with T2C2_HAEIF | P17743 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
           T2C2_HAEIF     2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKRRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDSELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
               SCOP domains d1xhvc_ C: Restriction en       donuclease HincII                                                                                                                                                                                                                SCOP domains
               CATH domains 1xhvC00 C:2-257  [code=3.       40.600.10, no name defined]                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..eee.....-------hhhhhhhhhhhhhhhh...eehhhhhhhhhhhh.......hhhhhh..hhhhhhhhh.hhhhhhh.-..............eeee.-..eeeeeeeeee........eeeehhhhhhhhhhhhhhh....eeeeeeeeeeeee..eeeeeeeeeee.hhh......ee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xhv C   2 SFIKPIYQDINSILIGQKVKRPKSG-------GEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENW-IENLFEEKQNDTADILLVK-QFYELLDVKTRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
                                    11        21    |    -  |     41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
                                                   26      34                                                               99 |               119 |                                                                                                                                        
                                                                                                                             101                 121

Chain D from PDB  Type:PROTEIN  Length:247
 aligned with T2C2_HAEIF | P17743 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
           T2C2_HAEIF     2 SFIKPIYQDINSILIGQKVKRPKSGTLSGHAAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKRRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDSELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
               SCOP domains d1xhvd_ D: Restrictio         n endonuclease HincII                                                                                                                                                                                                              SCOP domains
               CATH domains 1xhvD00 D:2-257  [cod         e=3.40.600.10, no name defined]                                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh......---------..hhhhhhhhhhhhhh.....eehhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.hhhhhhh................eeeee..eeeeeeeeeee........eeeehhhhhhhhhhhhhh.....eeeeeeeeeeeee..eeeeeeeeeee.hhhhhhhheee.....eee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xhv D   2 SFIKPIYQDINSILIGQKVKR---------AAGEPFEKLVYKFLKENLSDLTFKQYEYLNDLFMKNPAIIGHEARYKLFNSPTLLFLLSRGKAATENWSIENLFEEKQNDTADILLVKDQFYELLDVKTRNISKSAQAPNIISAYKLAQTCAKMIDNKEFDLFDINYLEVDWELNGEDLVCVSTSFAELFKSEPSELYINWAAAMQIQFHVRDLDQGFNGTREEWAKSYLKHFVTQAEQRAISMIDKFVKPFKKYI 257
                                    11        21|        -|       41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
                                               22        32

Chain E from PDB  Type:DNA  Length:7
                                       
                 1xhv E   1 GCCGGTC   7

Chain F from PDB  Type:DNA  Length:6
                                      
                 1xhv F   8 GACCGG  13

Chain G from PDB  Type:DNA  Length:7
                                       
                 1xhv G   1 GCCGGTC   7

Chain H from PDB  Type:DNA  Length:6
                                      
                 1xhv H   8 GACCGG  13

Chain I from PDB  Type:DNA  Length:7
                                       
                 1xhv I   1 GCCGGTC   7

Chain J from PDB  Type:DNA  Length:6
                                      
                 1xhv J   8 GACCGG  13

Chain K from PDB  Type:DNA  Length:7
                                       
                 1xhv K   1 GCCGGTC   7

Chain L from PDB  Type:DNA  Length:6
                                      
                 1xhv L   8 GACCGG  13

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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(

)

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 HincII (19)

Protein domain: Restriction endonuclease HincII (19)

Haemophilus influenzae [TaxId: 727] (19)

1a	d1xhva_	A:
1b	d1xhvb_	B:
1c	d1xhvc_	C:
1d	d1xhvd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: ECO RV Endonuclease; Chain A (56)

Homologous Superfamily: [code=3.40.600.10, no name defined] (55)

[unclassified] (40)

1a	1xhvC00	C:2-257
1b	1xhvD00	D:2-257
1c	1xhvB00	B:2-257
1d	1xhvA00	A:2-258

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (T2C2_HAEIF | P17743)

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: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 Unit
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	Cis Peptide Bonds
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	1xhv
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1kc6	HINCII BOUND TO COGNATE DNA GTCGAC
1tw8	HINCII BOUND TO COGNATE DNA GTCGAC AND CA2+
1xhu	HINCII BOUND TO CLEAVED COGNATE DNA GTCGAC

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 22)

Sites (22, 22)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

CATH Domains (1, 4)

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Gene Ontology (7, 7)

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