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(-) Description

Title :  CRYSTAL 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) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  A (4x),B (4x)
Biol. Unit 4:  A (4x),B (4x)
Biol. Unit 5:  A,B  (2x)
Biol. Unit 6:  A (1x),B (1x)
Biol. Unit 7:  A (1x),B (1x)
Biol. Unit 8:  A (1x),B (1x)
Biol. Unit 9:  A (1x),B (1x)
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
(for further references see the PDB file header)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x):  B
Biological Unit 2 (1x): A 
Biological Unit 3 (4x): A (4x)B (4x)
Biological Unit 4 (4x): A (4x)B (4x)
Biological Unit 5 (2x): AB
Biological Unit 6 (1x): A (1x)B (1x)
Biological Unit 7 (1x): A (1x)B (1x)
Biological Unit 8 (1x): A (1x)B (1x)
Biological Unit 9 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1ASN2Mod. Amino AcidASPARAGINE
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO42Ligand/IonSULFATE ION
4ZN4Ligand/IonZINC ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ASN1Mod. Amino AcidASPARAGINE
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO41Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1ASN1Mod. Amino AcidASPARAGINE
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO41Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (3, 12)
No.NameCountTypeFull Name
1ASN4Mod. Amino AcidASPARAGINE
2KCX4Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO44Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 4 (3, 12)
No.NameCountTypeFull Name
1ASN4Mod. Amino AcidASPARAGINE
2KCX4Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO44Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 5 (3, 12)
No.NameCountTypeFull Name
1ASN4Mod. Amino AcidASPARAGINE
2KCX4Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO44Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 6 (3, 3)
No.NameCountTypeFull Name
1ASN1Mod. Amino AcidASPARAGINE
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO41Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 7 (3, 3)
No.NameCountTypeFull Name
1ASN1Mod. Amino AcidASPARAGINE
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO41Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 8 (3, 3)
No.NameCountTypeFull Name
1ASN1Mod. Amino AcidASPARAGINE
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO41Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 9 (3, 3)
No.NameCountTypeFull Name
1ASN1Mod. Amino AcidASPARAGINE
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3SO41Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:70 , GLY B:74 , GLY B:75 , GLU B:77 , THR B:106 , TYR B:137 , SER B:289 , ASN B:401 , ZN B:603BINDING SITE FOR RESIDUE SO4 B 391
2AC2SOFTWAREHIS B:68 , HIS B:70 , KCX B:162 , ASP B:285 , SO4 B:391 , ASN B:401 , ZN B:604BINDING SITE FOR RESIDUE ZN B 603
3AC3SOFTWARETYR B:137 , KCX B:162 , HIS B:201 , HIS B:230 , ASN B:401 , ZN B:603BINDING SITE FOR RESIDUE ZN B 604
4AC4SOFTWAREHIS A:70 , GLY A:74 , GLY A:75 , GLU A:77 , GLY A:105 , THR A:106 , TYR A:137 , SER A:289 , HOH A:616BINDING SITE FOR RESIDUE SO4 A 391
5AC5SOFTWAREHIS A:68 , HIS A:70 , KCX A:162 , ASP A:285 , ZN A:602BINDING SITE FOR RESIDUE ZN A 601
6AC6SOFTWARETYR A:137 , KCX A:162 , HIS A:201 , HIS A:230 , ASN A:400 , ZN A:601BINDING SITE FOR RESIDUE ZN A 602
7AC7SOFTWARETYR B:137 , ARG B:169 , HIS B:201 , HIS B:230 , ARG B:233 , ASP B:285 , SER B:289 , SO4 B:391 , ZN B:603 , ZN B:604BINDING SITE FOR RESIDUE ASN B 401
8AC8SOFTWARETYR A:137 , ARG A:169 , HIS A:201 , ARG A:233 , ASP A:285 , ZN A:602BINDING SITE FOR RESIDUE ASN A 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1POK)

(-) Sequences/Alignments

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:378
 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 d1poka1 A:1-62,A:347-388 Isoaspartyl dipeptidase              d1poka2 A:63-346 Isoaspartyl dipeptidase, catalytic domain                                                                                                                                                                                                                                  d1poka1 A:1-62,A:347-388                  - SCOP domains
               CATH domains 1pokA01 A:1-63,A:343-388 Urease, subunit C, domain 1           1pokA02 A:64-342 Metal-dependent hydrolases                                                                                                                                                                                                                                            1pokA01 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....hhhhhhh..eeeeee.........hhhhhhhhhhhhhhh..eeeeee............hhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhh...hhh.eeeehhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh..hhh.eeee......-----------......hhhhhhhhhhhhhh...hhhhhhh..hhhhhhhh...............eeee.....eeeeee..eeee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pok A   1 MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVkCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSDGNGS-----------HIGVAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFEN 400
                                    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                                                                                                                        289         301                                                                                    388|
                                                                                                                                                                                                                                                                                                                                                                                                                              400


Chain B from PDB  Type:PROTEIN  Length:375
 aligned with IADA_ECOLI | P39377 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:391
                                                                                                                                                                                                                                                                                                                                                                                                                               390 
                                    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       390 
           IADA_ECOLI     1 MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVKCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSDGNGSQPFFDDEGNLTHIGVAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFETA-   -
               SCOP domains d1pokb1 B:1-62,B:347-388 Isoaspartyl dipeptidase              d1pokb2 B:63-346 Isoaspartyl dipeptidase, catalytic domain                                                                                                                                                                                                                                  d1pokb1 B:1-62,B:347-388                    - SCOP domains
               CATH domains 1pokB01 B:1-63,B:343-388 Urease, subunit C, domain 1           1pokB02 B:64-342 Metal-dependent hydrolases                                                                                                                                                                                                                                            1pokB01 B:1-63,B:343-388                        - CATH domains
           Pfam domains (1) ---------------------------Amidohydro_5-1pokB01 B:28-100                                            --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------Amidohydro_5-1pokB02 B:28-100                                            --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhheeeeeeeeee...eeeeeeeeee..eeeee...........eeeee....eeee.eeeeee.........hhhhh....hhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhh.eeeeee............hhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhh..hhh.eeeehhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhh.hhh.eeee......--------------...hhhhhhhhhhhhh....hhhhhhh..hhhhhhhh...............eeee.......eeee..eeee............--. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pok B   1 MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVkCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSDGNGS--------------VAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFE--N 401
                                    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                                                                                                                        289            304                                                                                 388  |
                                                                                                                                                                                                                                                                                                                                                                                                                                401
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (10, 10)

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.

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  1pok
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  3.4.19.-
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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

(-) Related Entries Specified in the PDB File

1po9 1poj