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(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI ISOASPARTYL DIPEPTIDASE MUTANT D285N COMPLEXED WITH BETA-ASPARTYLHISTIDINE
 
Authors :  R. Marti-Arbona, V. Fresquet, J. B. Thoden, M. L. Davis, H. M. Holden, F.
Date :  21 Dec 04  (Deposition) - 26 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Hydrolase, Dipeptidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Marti-Arbona, V. Fresquet, J. B. Thoden, M. L. Davis, H. M. Holden, F. M. Raushel
Mechanism Of The Reaction Catalyzed By Isoaspartyl Dipeptidase From Escherichia Coli.
Biochemistry V. 44 7115 2005
PubMed-ID: 15882050  |  Reference-DOI: 10.1021/BI050008R

(-) Compounds

Molecule 1 - ISOASPARTYL DIPEPTIDASE
    Chains: A
    EC Number: 3.4.19.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: IADA
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
 
Molecule 2 - ISOASPARTYL DIPEPTIDASE
    Chains: B
    EC Number: 3.4.19.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: IADA
    Mutation: YES
    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  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1BDH2Ligand/IonL-BETA-ASPARTYLHISTIDINE
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1BDH8Ligand/IonL-BETA-ASPARTYLHISTIDINE
2KCX4Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:68 , HIS A:70 , ASN A:285 , ZN A:392 , BDH A:393 , HOH A:508BINDING SITE FOR RESIDUE ZN A 391
2AC2SOFTWARETYR A:137 , HIS A:201 , HIS A:230 , ZN A:391 , BDH A:393 , HOH A:508BINDING SITE FOR RESIDUE ZN A 392
3AC3SOFTWAREGLY A:74 , GLY A:75 , GLU A:77 , GLY A:105 , THR A:106 , TYR A:137 , ARG A:169 , HIS A:201 , ARG A:233 , ASN A:285 , GLY A:288 , SER A:289 , PRO A:291 , ZN A:391 , ZN A:392 , HOH A:414BINDING SITE FOR RESIDUE BDH A 393
4AC4SOFTWAREHIS B:68 , HIS B:70 , KCX B:162 , ASN B:285 , ZN B:392 , BDH B:393BINDING SITE FOR RESIDUE ZN B 391
5AC5SOFTWARETYR B:137 , KCX B:162 , HIS B:201 , HIS B:230 , ZN B:391 , BDH B:393BINDING SITE FOR RESIDUE ZN B 392
6AC6SOFTWAREHIS B:70 , GLY B:74 , GLY B:75 , GLU B:77 , GLY B:105 , THR B:106 , TYR B:137 , KCX B:162 , ARG B:169 , HIS B:201 , HIS B:230 , ARG B:233 , ASN B:285 , SER B:289 , PRO B:291 , ZN B:391 , ZN B:392 , HOH B:483BINDING SITE FOR RESIDUE BDH B 393

(-) SS Bonds  (0, 0)

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

(-) 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 1YBQ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YBQ)

(-) 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: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 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1ybqA01 A:1-63,A:343-389 Urease, subunit C, domain 1           1ybqA02 A:64-342 Metal-dependent hydrolases                                                                                                                                                                                                                                            1ybqA01 A:1-63,A:343-389                        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..hhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhh...............eeee.....eeeeee..eeeee..ee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ybq A   1 MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVKCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSNGNGSQPFFDDEGNLTHIGVAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFET 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         


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 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1ybqB01 B:1-63,B:343-389 Urease, subunit C, domain 1           1ybqB02 B:64-342 Metal-dependent hydrolases                                                                                                                                                                                                                                            1ybqB01 B:1-63,B:343-389                        CATH domains
           Pfam domains (1) ---------------------------Amidohydro_5-1ybqB01 B:28-100                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------Amidohydro_5-1ybqB02 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......hhhhhhhhhh...hhh.eeeehhhhhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh..hhh.eeee........ee.....eee......hhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhh...............eeee.....eeeeee..eeeee..ee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ybq B   1 MIDYTAAGFTLLQGAHLYAPEDRGICDVLVANGKIIAVASNIPSDIVPNCTVVDLSGQILCPGFIDQHVHLIGGGGEAGPTTRTPEVALSRLTEAGVTSVVGLLGTDSISRHPESLLAKTRALNEEGISAWMLTGAYHVPSRTITGSVEKDVAIIDRVIGVkCAISDHRSAAPDVYHLANMAAESRVGGLLGGKPGVTVFHMGDSKKALQPIYDLLENCDVPISKLLPTHVNRNVPLFEQALEFARKGGTIDITSSIDEPVAPAEGIARAVQAGIPLARVTLSSNGNGSQPFFDDEGNLTHIGVAGFETLLETVQVLVKDYDFSISDALRPLTSSVAGFLNLTGKGEILPGNDADLLVMTPELRIEQVYARGKLMVKDGKACVKGTFET 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)
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  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  (0, 0)

(no "SCOP Domain" information available for 1YBQ)

(-) 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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  1ybq
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  IADA_ECOLI | P39377
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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 1pok 2aqo 2aqv

(-) Related Entries Specified in the PDB File

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