4ONW - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF DAPE PROTEIN FROM V.CHOLEREA

Authors :   B. Nocek, M. Makowska-Grzyska, R. Jedrzejczak, M. Gu, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious D (Csgid)

Date :   29 Jan 14 (Deposition) - 23 Apr 14 (Release) - 23 Jul 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Dape, M20, Aminopeptidase, Csgid, Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Zn Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Nocek, A. Starus, M. Makowska-Grzyska, B. Gutierrez, S. Sanchez, R. Jedrzejczak, J. C. Mack, K. W. Olsen, A. Joachimiak, R. C. Holz
The Dimerization Domain In Dape Enzymes Is Required For Catalysis.
Plos One V. 9 93593 2014
PubMed-ID: 24806882 | Reference-DOI: 10.1371/JOURNAL.PONE.0093593

Molecule 1 - SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE
	Chains	:	A, B
	EC Number	:	3.5.1.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	DAPE, VC_2152
	Organism Scientific	:	VIBRIO CHOLERAE O1 BIOVAR EL TOR
	Organism Taxid	:	243277
	Strain	:	N16961
	Synonym	:	SDAP DESUCCINYLASE, N-SUCCINYL-LL-2,6-DIAMINOHEPTANEDIOATE AMIDOHYDROLASE

		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 (4, 13)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	BU1	6	Ligand/Ion	1,4-BUTANEDIOL
3	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
4	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	BU1	2	Ligand/Ion	1,4-BUTANEDIOL
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 2 (4, 8)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	BU1	4	Ligand/Ion	1,4-BUTANEDIOL
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:145 , GLU A:148 , THR A:149 , HOH A:522 , ARG B:179 , HOH B:452	BINDING SITE FOR RESIDUE GOL A 401
02	AC2	SOFTWARE	MET A:151 , GLU A:155 , LEU A:156 , ILE A:157 , MET A:224 , GLY A:225 , ALA A:226 , HOH A:505	BINDING SITE FOR RESIDUE BU1 A 402
03	AC3	SOFTWARE	GLU A:40 , ARG A:55 , GLY A:57 , THR A:58 , HOH A:575	BINDING SITE FOR RESIDUE BU1 A 403
04	AC4	SOFTWARE	ARG A:56 , PRO A:121 , ASP A:122 , HIS A:123	BINDING SITE FOR RESIDUE EDO A 404
05	AC5	SOFTWARE	GLY A:67 , LEU A:130 , THR A:132 , THR A:143 , VAL A:162 , ASP A:217	BINDING SITE FOR RESIDUE EDO A 405
06	AC6	SOFTWARE	HIS A:81 , THR A:82 , VAL B:89 , ASP B:91 , GLY B:92 , HOH B:558	BINDING SITE FOR RESIDUE BU1 B 301
07	AC7	SOFTWARE	ARG A:179 , HOH A:550 , ARG B:145 , GLU B:148 , THR B:149 , HOH B:443	BINDING SITE FOR RESIDUE GOL B 302
08	AC8	SOFTWARE	VAL B:147 , MET B:151 , GLU B:155 , LEU B:156 , ILE B:157 , MET B:224 , GLY B:225 , ALA B:226 , HOH B:411	BINDING SITE FOR RESIDUE BU1 B 303
09	AC9	SOFTWARE	VAL A:89 , ASP A:91 , GLY A:92 , LEU B:77 , TRP B:80 , HIS B:81	BINDING SITE FOR RESIDUE BU1 B 304
10	BC1	SOFTWARE	GLU B:40 , ARG B:55 , GLY B:57 , HOH B:562	BINDING SITE FOR RESIDUE BU1 B 305
11	BC2	SOFTWARE	GLY B:178 , GLY B:214 , GLY B:218 , GLU B:230	BINDING SITE FOR RESIDUE ACT B 306
12	BC3	SOFTWARE	PRO B:121 , HIS B:123	BINDING SITE FOR RESIDUE EDO B 307
13	BC4	SOFTWARE	GLY B:67 , HIS B:68 , VAL B:162 , GLU B:164 , THR B:215 , ASP B:217 , HOH B:543	BINDING SITE FOR RESIDUE EDO B 308

(no "SS Bond" information available for 4ONW)

Asymmetric Unit

No.	Residues
1	Thr A:20	-	Pro A:21
2	Ser A:60	-	Pro A:61
3	Asp A:101	-	Met A:102
4	Thr B:20	-	Pro B:21
5	Ser B:60	-	Pro B:61
6	Asp B:101	-	Met B:102

(no "SAP(SNP)/Variant" information available for 4ONW)

(no "PROSITE Motif" information available for 4ONW)

(no "Exon" information available for 4ONW)

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
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh........hhhhhhhhhhhhh..eeeeeee..eeeeeeee.....eeeeeee.......hhhhh.......eee..eee......hhhhhhhhhhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhhh.....eeee...........eeee.hhhhhh....hhhhhhhhhhhhhhhh...eee....hhhhhhhhhhh.eeee.............eeehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4onw A   2 TDSPVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGTQSPLFVFAGHTDVVPAGPLSQWHTPPFEPTVIDGFLHGRGAADMKGSLACMIVAVERFIAEHPDHQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRGGGFLTDTGELLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADLEKLTDMYQKTLNHLLG 266
                                    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       261

Chain B from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.........hhhhhhhhhhhh...eeeeeee..eeeeeeee.....eeeeeee.......hhhhh.......eee..eee......hhhhhhhhhhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhh......eeee...........eeee.hhhhhh....hhhhhhhhhhhhhhhh...eee....hhhhhhhhhhh.eeee.............eeehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4onw B   2 TDSPVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGTQSPLFVFAGHTDVVPAGPLSQWHTPPFEPTVIDGFLHGRGAADMKGSLACMIVAVERFIAEHPDHQGSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRGGGFLTDTGELLAAVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADLEKLTDMYQKTLNHLLG 266
                                    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       261

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 '\|'

(no "SCOP Domain" information available for 4ONW)

(no "CATH Domain" information available for 4ONW)

(no "Pfam Domain" information available for 4ONW)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		BU1	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		BC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asp A:101 - Met A:102	[ RasMol ]
		Asp B:101 - Met B:102	[ RasMol ]
		Ser A:60 - Pro A:61	[ RasMol ]
		Ser B:60 - Pro B:61	[ RasMol ]
		Thr A:20 - Pro A:21	[ RasMol ]
		Thr B:20 - Pro B:21	[ RasMol ]

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

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	4onw
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		Orientation in Membranes	:	OPM
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	3.5.1.18
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	DAPE_VIBCH \| Q9KQ52	:	4op4

3isz	RELATED ID: CSGID-IDP90246 RELATED DB: TARGETTRACK

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (12, 12)

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