1PO9 - JenaLib

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Title :   CRYTSAL STRUCTURE OF ISOASPARTYL DIPEPTIDASE

Authors :   D. Jozic, J. T. Kaiser, R. Huber, W. Bode, K. Maskos

Date :   15 Jun 03 (Deposition) - 22 Jun 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (4x)

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

Reference :   D. Jozic, J. T. Kaiser, R. Huber, W. Bode, K. Maskos
X-Ray Structure Of Isoaspartyl Dipeptidase From E. Coli: A Dinuclear Zinc Peptidase Evolved From Amidohydrolases.
J. Mol. Biol. V. 332 243 2003
PubMed-ID: 12946361 | Reference-DOI: 10.1016/S0022-2836(03)00845-3

Molecule 1 - ISOASPARTYL DIPEPTIDASE
	Chains	:	A, B
	EC Number	:	3.4.19.-
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (4x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

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

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

Biological Unit 3 (1, 8)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:68 , HIS A:70 , KCX A:162 , ASP A:285 , ZN A:602 , HOH A:774	BINDING SITE FOR RESIDUE ZN A 601
2	AC2	SOFTWARE	TYR A:137 , KCX A:162 , HIS A:201 , HIS A:230 , ZN A:601 , HOH A:774	BINDING SITE FOR RESIDUE ZN A 602
3	AC3	SOFTWARE	HIS B:68 , HIS B:70 , KCX B:162 , ASP B:285 , ZN B:604 , HOH B:624	BINDING SITE FOR RESIDUE ZN B 603
4	AC4	SOFTWARE	TYR B:137 , KCX B:162 , HIS B:201 , HIS B:230 , ZN B:603 , HOH B:624	BINDING SITE FOR RESIDUE ZN B 604

(no "SS Bond" information available for 1PO9)

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 1PO9)

(no "PROSITE Motif" information available for 1PO9)

(no "Exon" information available for 1PO9)

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:373
 aligned with IADA_ECOLI | P39377 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:388
                                    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 MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVKCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSDGNGSQPFFDDEGNLTHIGVAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFE 388
               SCOP domains d1po9a1 A:1-62,A:347-388 Isoaspartyl dipeptidase              d1po9a2 A:63-346 Isoaspartyl dipeptidase, catalytic domain                                                                                                                                                                                                                                  d1po9a1 A:1-62,A:347-388                   SCOP domains
               CATH domains 1po9A01 A:1-63,A:343-388 Urease, subunit C, domain 1           1po9A02 A:64-342 Metal-dependent hydrolases                                                                                                                                                                                                                                            1po9A01 A:1-63,A:343-388                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.eeee..eee...eeee.eeeee..eeeeee...........eeee....eeee.eeeeee.........hhhhh....hhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhh.eeeeeee...........hhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhh..hhh.eeeehhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh..hhh.eeee.....---------------...hhhhhhhhhhhhhh...hhhhhhh..hhhhhhhh...............eeee.....eeeeee..eeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1po9 A   1 MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVkCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSDGNG---------------VAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFE 388
                                    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       | -         -   |   310       320       330       340       350       360       370       380        
                                                                                                                                                                                           162-KCX                                                                                                                       288             304

Chain B from PDB  Type:PROTEIN  Length:373
 aligned with IADA_ECOLI | P39377 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:388
                                    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 MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVKCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSDGNGSQPFFDDEGNLTHIGVAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFE 388
               SCOP domains d1po9b1 B:1-62,B:347-388 Isoaspartyl dipeptidase              d1po9b2 B:63-346 Isoaspartyl dipeptidase, catalytic domain                                                                                                                                                                                                                                  d1po9b1 B:1-62,B:347-388                   SCOP domains
               CATH domains 1po9B01 B:1-63,B:343-388 Urease, subunit C, domain 1           1po9B02 B:64-342 Metal-dependent hydrolases                                                                                                                                                                                                                                            1po9B01 B:1-63,B:343-388                       CATH domains
           Pfam domains (1) ---------------------------Amidohydro_5-1po9B01 B:28-100                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ---------------------------Amidohydro_5-1po9B02 B:28-100                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ...hhhhh.eeee..eee...eeee.eeeee..eeeeee...........eeee....eeee.eeeeee.........hhhhh....hhhhhhh..eeeeee.........hhhhhhhhhhhhhhhh.eeeeeee...........hhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhh..hhh.eeeehhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh..hhh.eeee.....---------------....hhhhhhhhhhhhhh..hhhhhhh..hhhhhhhh...............eeee.....eeeeee..eeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1po9 B   1 MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVkCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSDGNG---------------VAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFE 388
                                    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       | -         -   |   310       320       330       340       350       360       370       380        
                                                                                                                                                                                           162-KCX                                                                                                                       288             304

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 (3)

1a	1po9A02	A:64-342
1b	1po9B02	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 (3)

2a	1po9A01	A:1-63,A:343-388
2b	1po9B01	B:1-63,B:343-388

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Amidohydrolase (126)

Family: Amidohydro_5 (8)

Escherichia coli (strain K12) (6)

1a	Amidohydro_5-1po9B01	B:28-100
1b	Amidohydro_5-1po9B02	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
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	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 Units
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	1po9
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	3.4.19.-
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	IADA_ECOLI \| P39377	:	1onw 1onx 1poj 1pok 1ybq 2aqo 2aqv

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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