1ONX - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ISOASPARTYL DIPEPTIDASE FROM ESCHERICHIA COLI COMPLEXED WITH ASPARTATE

Authors :   J. B. Thoden, R. Marti-Arbona, F. M. Raushel, H. M. Holden

Date :   02 Mar 03 (Deposition) - 06 May 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)

Keywords :   Amidohydrolase, Hydrolase, Metalloprotease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. B. Thoden, R. Marti-Arbona, F. M. Raushel, H. M. Holden
High Resolution X-Ray Structure Of Isoaspartyl Dipeptidase From Escherichia Coli
Biochemistry V. 42 4874 2003
PubMed-ID: 12718528 | Reference-DOI: 10.1021/BI034233P

Molecule 1 - ISOASPARTYL DIPEPTIDASE
	Chains	:	A, B
	EC Number	:	3.4.19.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)STAR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	IADA OR B4328
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	ASP	2	Mod. Amino Acid	ASPARTIC ACID
2	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 16)

No.	Name	Count	Type	Full Name
1	ASP	8	Mod. Amino Acid	ASPARTIC ACID
2	KCX	8	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:68 , HIS A:70 , KCX A:162 , ASP A:285 , ASP A:450	BINDING SITE FOR RESIDUE ZN A 401
2	AC2	SOFTWARE	TYR A:137 , KCX A:162 , HIS A:201 , HIS A:230 , ASP A:450	BINDING SITE FOR RESIDUE ZN A 402
3	AC3	SOFTWARE	HIS B:68 , HIS B:70 , KCX B:162 , ASP B:285 , ZN B:502 , ASP B:550	BINDING SITE FOR RESIDUE ZN B 501
4	AC4	SOFTWARE	TYR B:137 , KCX B:162 , HIS B:201 , HIS B:230 , ZN B:501 , ASP B:550	BINDING SITE FOR RESIDUE ZN B 502
5	AC5	SOFTWARE	GLY A:74 , GLY A:75 , GLU A:77 , GLY A:105 , THR A:106 , TYR A:137 , KCX A:162 , HIS A:201 , ASP A:285 , GLY A:288 , SER A:289 , ZN A:401 , ZN A:402 , HOH A:477	BINDING SITE FOR RESIDUE ASP A 450
6	AC6	SOFTWARE	GLY B:74 , GLY B:75 , GLU B:77 , GLY B:105 , THR B:106 , TYR B:137 , KCX B:162 , HIS B:201 , ASP B:285 , GLY B:288 , SER B:289 , HOH B:474 , ZN B:501 , ZN B:502	BINDING SITE FOR RESIDUE ASP B 550

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

Asymmetric Unit

No.	Residues
1	Ala A:19	-	Pro A:20
2	Val A:139	-	Pro A:140
3	Glu A:259	-	Pro A:260
4	Ala B:19	-	Pro B:20
5	Val B:139	-	Pro B:140
6	Glu B:259	-	Pro B:260

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

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

(no "Exon" information available for 1ONX)

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:389
 aligned with IADA_ECOLI | P39377 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:389
                                    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       330       340       350       360       370       380         
           IADA_ECOLI     1 MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVKCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSDGNGSQPFFDDEGNLTHIGVAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFET 389
               SCOP domains d1onxa1 A:1-62,A:347-389 Isoaspartyl dipeptidase              d1onxa2 A:63-346 Isoaspartyl dipeptidase, catalytic domain                                                                                                                                                                                                                                  d1onxa1 A:1-62,A:347-389                    SCOP domains
               CATH domains 1onxA01 A:1-63,A:343-382 Urease, subunit C, domain 1           1onxA02 A:64-342 Metal-dependent hydrolases                                                                                                                                                                                                                                            1onxA01 A:1-63,A:343-382                ------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.eeeeeeeee...eeeeeeeeee..eeeeee...........eeee....eeee.eeeeee.........hhhhh....hhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhh.eeeeeee...........hhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhh...hhh.eeeehhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh..hhh.eeee.....eeeee.....eeeeee...hhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhh...............eeee.....eeeeee..eeeee..ee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1onx A   1 MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVkCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSDGNGSQPFFDDEGNLTHIGVAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFET 389
                                    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       330       340       350       360       370       380         
                                                                                                                                                                                           162-KCX

Chain B from PDB  Type:PROTEIN  Length:389
 aligned with IADA_ECOLI | P39377 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:389
                                    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       330       340       350       360       370       380         
           IADA_ECOLI     1 MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVKCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSDGNGSQPFFDDEGNLTHIGVAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFET 389
               SCOP domains d1onxb1 B:1-62,B:347-389 Isoaspartyl dipeptidase              d1onxb2 B:63-346 Isoaspartyl dipeptidase, catalytic domain                                                                                                                                                                                                                                  d1onxb1 B:1-62,B:347-389                    SCOP domains
               CATH domains 1onxB01 B:1-63,B:343-389 Urease, subunit C, domain 1           1onxB02 B:64-342 Metal-dependent hydrolases                                                                                                                                                                                                                                            1onxB01 B:1-63,B:343-389                        CATH domains
           Pfam domains (1) ---------------------------Amidohydro_5-1onxB01 B:28-100                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------Amidohydro_5-1onxB02 B:28-100                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhh.eeeeeeeee...eeeeeeeeee..eeeeee...........eeee....eeee.eeeeee.........hhhhh....hhhhhhh..eeeeee.........hhhhhhhhhhhhhhh..eeeeeee...........hhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhh...hhh.eeeehhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh..hhh.eeee.....eeeee.....eeeeee...hhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhh...............eeee.....eeeeee..eeeee..ee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1onx B   1 MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVkCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSDGNGSQPFFDDEGNLTHIGVAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFET 389
                                    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       330       340       350       360       370       380         
                                                                                                                                                                                           162-KCX

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Metal-dependent hydrolases (190)

Escherichia coli. Organism_taxid: 562. (27)

1a	1onxA02	A:64-342
1b	1onxB02	B:64-342

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Urease, subunit C; domain 1 (95)

Homologous Superfamily: Urease, subunit C, domain 1 (95)

Escherichia coli. Organism_taxid: 562. (12)

2a	1onxB01	B:1-63,B:343-389
2b	1onxA01	A:1-63,A:343-382

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Amidohydrolase (126)

Family: Amidohydro_5 (8)

Escherichia coli (strain K12) (6)

1a	Amidohydro_5-1onxB01	B:28-100
1b	Amidohydro_5-1onxB02	B:28-100

Asymmetric Unit(hide GO term definitions)

Chain A,B (IADA_ECOLI | P39377)

molecular function
	GO:0008798	beta-aspartyl-peptidase activity	Catalysis of the cleavage of a beta-linked aspartic residue from the N-terminus of a polypeptide.
	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:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ASP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		KCX	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:19 - Pro A:20	[ RasMol ]
		Ala B:19 - Pro B:20	[ RasMol ]
		Glu A:259 - Pro A:260	[ RasMol ]
		Glu B:259 - Pro B:260	[ RasMol ]
		Val A:139 - Pro A:140	[ RasMol ]
		Val B:139 - Pro B:140	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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)

Access by PDB/NDB ID
	1onx
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	IADA_ECOLI \| P39377
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.4.19.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	IADA_ECOLI \| P39377
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	IADA_ECOLI \| P39377	:	1onw 1po9 1poj 1pok 1ybq 2aqo 2aqv

1onw	SAME PROTEIN IN UNCOMPLEXED FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (1, 2)

Gene Ontology (10, 10)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File