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(-) Description

Title :  CRYSTAL STRUCTURE OF ISOASPARTYL DIPEPTIDASE FROM E. COLI
 
Authors :  J. B. Thoden, R. Marti-Arbona, F. M. Raushel, H. M. Holden
Date :  02 Mar 03  (Deposition) - 06 May 03  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
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

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Asymmetric Unit (6, 14)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4MG1Ligand/IonMAGNESIUM ION
5NA1Ligand/IonSODIUM ION
6ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 20)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO12Ligand/Ion1,2-ETHANEDIOL
3KCX8Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4MG-1Ligand/IonMAGNESIUM ION
5NA-1Ligand/IonSODIUM ION
6ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:68 , HIS A:70 , KCX A:162 , ASP A:285 , ZN A:801 , HOH A:841BINDING SITE FOR RESIDUE ZN A 800
02AC2SOFTWARETYR A:137 , KCX A:162 , HIS A:201 , HIS A:230 , ZN A:800 , HOH A:841BINDING SITE FOR RESIDUE ZN A 801
03AC3SOFTWAREHIS B:68 , HIS B:70 , KCX B:162 , ASP B:285 , ZN B:803 , HOH B:864BINDING SITE FOR RESIDUE ZN B 802
04AC4SOFTWARETYR B:137 , KCX B:162 , HIS B:201 , HIS B:230 , ZN B:802 , HOH B:864BINDING SITE FOR RESIDUE ZN B 803
05AC5SOFTWAREHOH B:978 , HOH B:979 , HOH B:991 , HOH B:1003BINDING SITE FOR RESIDUE MG B 804
06AC6SOFTWAREHOH A:886 , GLY B:193 , EDO B:807 , HOH B:869 , HOH B:998 , HOH B:1052 , HOH B:1107BINDING SITE FOR RESIDUE NA B 805
07AC7SOFTWARELEU A:89 , GLY A:385 , HOH A:918BINDING SITE FOR RESIDUE CL A 802
08AC8SOFTWAREALA B:88 , LEU B:89 , GLY B:385BINDING SITE FOR RESIDUE CL B 806
09AC9SOFTWAREASP A:167 , HIS A:168 , ASP A:204BINDING SITE FOR RESIDUE CL A 803
10BC1SOFTWAREALA A:153 , LEU A:191 , HOH A:839 , HOH A:964 , ALA B:118 , ARG B:121BINDING SITE FOR RESIDUE EDO A 804
11BC2SOFTWARELEU A:117 , ALA A:118 , ARG A:121 , HOH A:848 , HOH A:970 , ALA B:153 , LEU B:191BINDING SITE FOR RESIDUE EDO A 805
12BC3SOFTWARETRP B:131 , GLY B:193 , PRO B:195 , ASN B:341 , LEU B:342 , NA B:805 , HOH B:869 , HOH B:989BINDING SITE FOR RESIDUE EDO B 807

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ONW)

(-) 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:376
 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 d1onwa1 A:1-62,A:347-389 Isoaspartyl dipeptidase              d1onwa2 A:63-346 Isoaspartyl dipeptidase, catalytic domain                                                                                                                                                                                                                                  d1onwa1 A:1-62,A:347-389                    SCOP domains
               CATH domains 1onwA01 A:1-63,A:343-389 Urease, subunit C, domain 1           1onwA02 A:64-342 Metal-dependent hydrolases                                                                                                                                                                                                                                            1onwA01 A:1-63,A:343-389                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.eeee..eee...eeee.eeeee..eeeeee...........eeee....eeee.eeeeee.........hhhhh....hhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhh.eeeee.............hhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhh...hhh.eeeehhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh..hhh.eeee......-------------.....hhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhh...............eeee.....eeeeee..eeeee..ee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1onw A   1 MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVkCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSDGNGS-------------GVAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFET 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        |-         -  |    310       320       330       340       350       360       370       380         
                                                                                                                                                                                           162-KCX                                                                                                                        289           303                                                                                      


Chain B from PDB  Type:PROTEIN  Length:380
 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 d1onwb1 B:1-62,B:347-389 Isoaspartyl dipeptidase              d1onwb2 B:63-346 Isoaspartyl dipeptidase, catalytic domain                                                                                                                                                                                                                                  d1onwb1 B:1-62,B:347-389                    SCOP domains
               CATH domains 1onwB01 B:1-63,B:343-389 Urease, subunit C, domain 1           1onwB02 B:64-342 Metal-dependent hydrolases                                                                                                                                                                                                                                            1onwB01 B:1-63,B:343-389                        CATH domains
           Pfam domains (1) ---------------------------Amidohydro_5-1onwB01 B:28-100                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------Amidohydro_5-1onwB02 B:28-100                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhh.eeee..eee...eeee.eeeee..eeeeee...........eeee....eeee.eeeeee.........hhhhh....hhhhhhhh.eeeeee.........hhhhhhhhhhhhhhhh.eeeee.............hhhhhhhhh..eeeeeeee........hhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhh...hhh.eeeehhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh..hhh.eeee.....ee.---------..ee..hhhhhhhhhhhhhhh..hhhhhhh..hhhhhhhh...............eeee.....eeeeee..eeeee..ee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1onw B   1 MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVkCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSDGNGSQP---------HIGVAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFET 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|        -|      310       320       330       340       350       360       370       380         
                                                                                                                                                                                           162-KCX                                                                                                                          291       301
   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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1ONW)