1YIX - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF YCFH, TATD HOMOLOG FROM ESCHERICHIA COLI K12, AT 1.9 A RESOLUTION

Authors :   V. N. Malashkevich, D. F. Xiang, F. M. Raushel, S. C. Almo, S. K. Burley, N Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   13 Jan 05 (Deposition) - 25 Jan 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Ycfh, Tim Barrel, Deoxyribonuclease, Zinc Ion, New York Sgx Research Center For Structural Genomics, Nysgxrc, Structural Genomics, Psi, Protein Structure Initiative, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. N. Malashkevich, D. F. Xiang, F. M. Raushel, S. C. Almo
Crystal Structure Of Ycfh, Tatd Homolog From Escherichia Coli
To Be Published
PubMed: search

Molecule 1 - DEOXYRIBONUCLEASE YCFH
	Chains	:	A, B
	EC Number	:	3.1.21.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	DL21
	Expression System Taxid	:	562
	Gene	:	YCFH
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

		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 (1, 4)

No.	Name	Count	Type	Full Name
1	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:7 , HIS A:9 , GLU A:94 , HIS A:155 , ASP A:205 , ZN A:604	BINDING SITE FOR RESIDUE ZN A 601
2	AC2	SOFTWARE	HIS B:7 , HIS B:9 , GLU B:94 , HIS B:155 , ASP B:205 , ZN B:603	BINDING SITE FOR RESIDUE ZN B 602
3	AC3	SOFTWARE	GLU B:94 , HIS B:130 , HIS B:155 , ZN B:602 , HOH B:636	BINDING SITE FOR RESIDUE ZN B 603
4	AC4	SOFTWARE	GLU A:94 , HIS A:130 , HIS A:155 , ZN A:601 , HOH A:863	BINDING SITE FOR RESIDUE ZN A 604

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

Asymmetric Unit

No.	Residues
1	Gly A:93	-	Glu A:94
2	Ser A:206	-	Pro A:207
3	Val A:212	-	Pro A:213
4	Gly B:93	-	Glu B:94
5	Ser B:206	-	Pro B:207
6	Val B:212	-	Pro B:213

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TATD_1	PS01137	TatD deoxyribonuclease family signature 1.	YCFH_ECO57	3-11	2	A:3-11 B:3-11
				YCFH_ECOL6	3-11	2	A:3-11 B:3-11
				YCFH_ECOLI	3-11	2	A:3-11 B:3-11
2	TATD_3	PS01091	TatD deoxyribonuclease family signature 3.	YCFH_ECO57	191-207	2	A:191-207 B:191-207
				YCFH_ECOL6	191-207	2	A:191-207 B:191-207
				YCFH_ECOLI	191-207	2	A:191-207 B:191-207

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TATD_1	PS01137	TatD deoxyribonuclease family signature 1.	YCFH_ECO57	3-11	1	A:3-11 -
				YCFH_ECOL6	3-11	1	A:3-11 -
				YCFH_ECOLI	3-11	1	A:3-11 -
2	TATD_3	PS01091	TatD deoxyribonuclease family signature 3.	YCFH_ECO57	191-207	1	A:191-207 -
				YCFH_ECOL6	191-207	1	A:191-207 -
				YCFH_ECOLI	191-207	1	A:191-207 -

Biological Unit 2 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TATD_1	PS01137	TatD deoxyribonuclease family signature 1.	YCFH_ECO57	3-11	1	- B:3-11
				YCFH_ECOL6	3-11	1	- B:3-11
				YCFH_ECOLI	3-11	1	- B:3-11
2	TATD_3	PS01091	TatD deoxyribonuclease family signature 3.	YCFH_ECO57	191-207	1	- B:191-207
				YCFH_ECOL6	191-207	1	- B:191-207
				YCFH_ECOLI	191-207	1	- B:191-207

(no "Exon" information available for 1YIX)

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:265
 aligned with YCFH_ECO57 | P0AFQ9 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:265
                                    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     
           YCFH_ECO57     1 MFLVDSHCHLDGLDYESLHKDVDDVLAKAAARDVKFCLAVATTLPGYLHMRDLVGERDNVVFSCGVHPLNQNDPYDVEDLRRLAAEEGVVALGETGLDYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRDARADTLAILREEKVTDCGGVLHCFTEDRETAGKLLDLGFYISFSGIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGVAVEELAQVTTDNFARLFHIDASRLQSIR 265
               SCOP domains d1yixa1 A:1-265 Putative deoxyribonuclease YcfH                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhh.......hhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhh....eeeee...........hhhhhhhhhh...eeeeeeeeee......hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eee.....hhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhh.eee.................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --TATD_1   -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATD_3           ---------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yix A   1 MFLVDSHCHLDGLDYESLHKDVDDVLAKAAARDVKFCLAVATTLPSYLHMRDLVGERDNVVFSCGVHPLNQNDPYDVEDLRRLAAEEGVVALGETGLDYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRDARADTLAILREEKVTDCGGVLHCFTEDRETAGKLLDLGFYISFSGIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGVAVEELAQVTTDNFARLFHIDASRLQSIR 265
                                    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

Chain A from PDB  Type:PROTEIN  Length:265
 aligned with YCFH_ECOL6 | P0AFQ8 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:265
                                    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     
           YCFH_ECOL6     1 MFLVDSHCHLDGLDYESLHKDVDDVLAKAAARDVKFCLAVATTLPGYLHMRDLVGERDNVVFSCGVHPLNQNDPYDVEDLRRLAAEEGVVALGETGLDYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRDARADTLAILREEKVTDCGGVLHCFTEDRETAGKLLDLGFYISFSGIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGVAVEELAQVTTDNFARLFHIDASRLQSIR 265
               SCOP domains d1yixa1 A:1-265 Putative deoxyribonuclease YcfH                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhh.......hhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhh....eeeee...........hhhhhhhhhh...eeeeeeeeee......hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eee.....hhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhh.eee.................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --TATD_1   -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATD_3           ---------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yix A   1 MFLVDSHCHLDGLDYESLHKDVDDVLAKAAARDVKFCLAVATTLPSYLHMRDLVGERDNVVFSCGVHPLNQNDPYDVEDLRRLAAEEGVVALGETGLDYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRDARADTLAILREEKVTDCGGVLHCFTEDRETAGKLLDLGFYISFSGIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGVAVEELAQVTTDNFARLFHIDASRLQSIR 265
                                    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

Chain A from PDB  Type:PROTEIN  Length:265
 aligned with YCFH_ECOLI | P0AFQ7 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:265
                                    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     
           YCFH_ECOLI     1 MFLVDSHCHLDGLDYESLHKDVDDVLAKAAARDVKFCLAVATTLPGYLHMRDLVGERDNVVFSCGVHPLNQNDPYDVEDLRRLAAEEGVVALGETGLDYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRDARADTLAILREEKVTDCGGVLHCFTEDRETAGKLLDLGFYISFSGIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGVAVEELAQVTTDNFARLFHIDASRLQSIR 265
               SCOP domains d1yixa1 A:1-265 Putative deoxyribonuclease YcfH                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeehhhhh.......hhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhh....eeeee...........hhhhhhhhhh...eeeeeeeeee......hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eee.....hhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhh.eee.................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --TATD_1   -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATD_3           ---------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yix A   1 MFLVDSHCHLDGLDYESLHKDVDDVLAKAAARDVKFCLAVATTLPSYLHMRDLVGERDNVVFSCGVHPLNQNDPYDVEDLRRLAAEEGVVALGETGLDYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRDARADTLAILREEKVTDCGGVLHCFTEDRETAGKLLDLGFYISFSGIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGVAVEELAQVTTDNFARLFHIDASRLQSIR 265
                                    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

Chain B from PDB  Type:PROTEIN  Length:265
 aligned with YCFH_ECO57 | P0AFQ9 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:265
                                    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     
           YCFH_ECO57     1 MFLVDSHCHLDGLDYESLHKDVDDVLAKAAARDVKFCLAVATTLPGYLHMRDLVGERDNVVFSCGVHPLNQNDPYDVEDLRRLAAEEGVVALGETGLDYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRDARADTLAILREEKVTDCGGVLHCFTEDRETAGKLLDLGFYISFSGIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGVAVEELAQVTTDNFARLFHIDASRLQSIR 265
               SCOP domains d1yixb_ B: automated matches                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---TatD_DNase-1yixB01 B:4-255                                                                                                                                                                                                                                  ---------- Pfam domains (1)
           Pfam domains (2) ---TatD_DNase-1yixB02 B:4-255                                                                                                                                                                                                                                  ---------- Pfam domains (2)
         Sec.struct. author ..eeeeeehhhhh.......hhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhh....eeeee...........hhhhhhhhh....eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eee.....hhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhh.eee.................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --TATD_1   -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATD_3           ---------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yix B   1 MFLVDSHCHLDGLDYESLHKDVDDVLAKAAARDVKFCLAVATTLPSYLHMRDLVGERDNVVFSCGVHPLNQNDPYDVEDLRRLAAEEGVVALGETGLDYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRDARADTLAILREEKVTDCGGVLHCFTEDRETAGKLLDLGFYISFSGIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGVAVEELAQVTTDNFARLFHIDASRLQSIR 265
                                    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

Chain B from PDB  Type:PROTEIN  Length:265
 aligned with YCFH_ECOL6 | P0AFQ8 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:265
                                    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     
           YCFH_ECOL6     1 MFLVDSHCHLDGLDYESLHKDVDDVLAKAAARDVKFCLAVATTLPGYLHMRDLVGERDNVVFSCGVHPLNQNDPYDVEDLRRLAAEEGVVALGETGLDYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRDARADTLAILREEKVTDCGGVLHCFTEDRETAGKLLDLGFYISFSGIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGVAVEELAQVTTDNFARLFHIDASRLQSIR 265
               SCOP domains d1yixb_ B: automated matches                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---TatD_DNase-1yixB01 B:4-255                                                                                                                                                                                                                                  ---------- Pfam domains (1)
           Pfam domains (2) ---TatD_DNase-1yixB02 B:4-255                                                                                                                                                                                                                                  ---------- Pfam domains (2)
         Sec.struct. author ..eeeeeehhhhh.......hhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhh....eeeee...........hhhhhhhhh....eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eee.....hhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhh.eee.................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --TATD_1   -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATD_3           ---------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yix B   1 MFLVDSHCHLDGLDYESLHKDVDDVLAKAAARDVKFCLAVATTLPSYLHMRDLVGERDNVVFSCGVHPLNQNDPYDVEDLRRLAAEEGVVALGETGLDYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRDARADTLAILREEKVTDCGGVLHCFTEDRETAGKLLDLGFYISFSGIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGVAVEELAQVTTDNFARLFHIDASRLQSIR 265
                                    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

Chain B from PDB  Type:PROTEIN  Length:265
 aligned with YCFH_ECOLI | P0AFQ7 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:265
                                    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     
           YCFH_ECOLI     1 MFLVDSHCHLDGLDYESLHKDVDDVLAKAAARDVKFCLAVATTLPGYLHMRDLVGERDNVVFSCGVHPLNQNDPYDVEDLRRLAAEEGVVALGETGLDYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRDARADTLAILREEKVTDCGGVLHCFTEDRETAGKLLDLGFYISFSGIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGVAVEELAQVTTDNFARLFHIDASRLQSIR 265
               SCOP domains d1yixb_ B: automated matches                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---TatD_DNase-1yixB01 B:4-255                                                                                                                                                                                                                                  ---------- Pfam domains (1)
           Pfam domains (2) ---TatD_DNase-1yixB02 B:4-255                                                                                                                                                                                                                                  ---------- Pfam domains (2)
         Sec.struct. author ..eeeeeehhhhh.......hhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhh....eeeee...........hhhhhhhhh....eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eee.....hhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhh.eee.................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --TATD_1   -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATD_3           ---------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yix B   1 MFLVDSHCHLDGLDYESLHKDVDDVLAKAAARDVKFCLAVATTLPSYLHMRDLVGERDNVVFSCGVHPLNQNDPYDVEDLRRLAAEEGVVALGETGLDYYYTPETKVRQQESFIHHIQIGRELNKPVIVHTRDARADTLAILREEKVTDCGGVLHCFTEDRETAGKLLDLGFYISFSGIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGVAVEELAQVTTDNFARLFHIDASRLQSIR 265
                                    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

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Metallo-dependent hydrolases (273)

Family: automated matches (44)

Protein domain: automated matches (44)

Escherichia coli K-12 [TaxId: 83333] (1)

d1yixb_

Family: TatD Mg-dependent DNase-like (4)

Protein domain: Putative deoxyribonuclease YcfH (1)

Escherichia coli [TaxId: 562] (1)

d1yixa1

A:1-265

(no "CATH Domain" information available for 1YIX)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Amidohydrolase (126)

Family: TatD_DNase (6)

Escherichia coli (strain K12) (3)

1a	TatD_DNase-1yixB01	B:4-255
1b	TatD_DNase-1yixB02	B:4-255

Asymmetric Unit(hide GO term definitions)

Chain A,B (YCFH_ECOLI | P0AFQ7)

molecular function
	GO:0004536	deoxyribonuclease activity	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
	GO:0016888	endodeoxyribonuclease activity, producing 5'-phosphomonoesters	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
	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:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006308	DNA catabolic process	The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain A,B (YCFH_ECOL6 | P0AFQ8)

molecular function
	GO:0004536	deoxyribonuclease activity	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
	GO:0016888	endodeoxyribonuclease activity, producing 5'-phosphomonoesters	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
	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:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.

Chain A,B (YCFH_ECO57 | P0AFQ9)

molecular function
	GO:0004536	deoxyribonuclease activity	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
	GO:0016888	endodeoxyribonuclease activity, producing 5'-phosphomonoesters	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
	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:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.

Asymmetric Unit
	Complete Structure
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	Cis Peptide Bonds
		Gly A:93 - Glu A:94	[ RasMol ]
		Gly B:93 - Glu B:94	[ RasMol ]
		Ser A:206 - Pro A:207	[ RasMol ]
		Ser B:206 - Pro B:207	[ RasMol ]
		Val A:212 - Pro A:213	[ RasMol ]
		Val B:212 - Pro B:213	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

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	1yix
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	YCFH_ECOL6 \| P0AFQ8
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	YCFH_ECOLI \| P0AFQ7
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	3.1.21.-
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(no "Entries Sharing at Least One Protein Chain" available for 1YIX)

1j6o	TATD HOMOLOG FROM THERMOTOGA MARITIMA RELATED ID: NYSGXRC-T2214 RELATED DB: TARGETDB
1xwy	TATD DEOXYRIBONUCLEASE FROM E. COLI

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (8, 19)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File