Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF AMINOPEPTIDASE I FROM BORRELIA BURGDORFERI B31
 
Authors :  T. Min, J. Gorman, L. Shapiro, S. K. Burley, New York Sgx Research Ce Structural Genomics (Nysgxrc)
Date :  08 Dec 04  (Deposition) - 04 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (12x)
Keywords :  Aminopeptidase I, Borrelia Burgdorferi B31, Ysci, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Min, J. Gorman, L. Shapiro
The Crystal Structure Of Aminopeptidase I (Ysci) From Borrelia Burgdorferi
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE M18-FAMILY AMINOPEPTIDASE 1
    Chains: A
    EC Number: 3.4.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET26B
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: APEA
    Organism Common: LYME DISEASE SPIROCHETE
    Organism Scientific: BORRELIA BURGDORFERI
    Organism Taxid: 139

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (12x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 84)
No.NameCountTypeFull Name
1MSE84Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1Y7E)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y7E)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:341 -Pro A:342

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y7E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y7E)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y7E)

(-) 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:404
 aligned with APEA_BORBU | P0C925 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:455
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453     
           APEA_BORBU     4 QNPWIYLNEEEKNQILNFSESYKKFISKFKTEREVTAYALDKAKKLGFINAEEKKNLMPGDKIFYTCREKSVAFAIIGKNPIEDGMNFIVSHTDSPRLDAKPSPISEENELTFIKTNYYGGIKKYQWLSTPLSIRGVVFLKNGEKVEINIGDNENDPVFVIPDILPHLDRKIQRNKKSDEIVEGENLKILIGSLPIETKEKNKVKLATLQLIKEKYKIEEEDFVSSEIEIVPAGTAKDVGFDKALIGAYGQDDKICVFTSLESIFDLEETPNKTAICFLVDKEEIGSTGSTGLDSRYLEYFVSDMIFKIKKSEYNNLHVQKALWNSKSISADVCAAINPLFSSVHDEQNAPQLGYGIPIMKYTGHGGKSMASDADAELVSYIRQLLNKNNIAWQVATLGKVEEGGGGTVAKFLAGYGIRTIDMGPAVISMHSPMEITSKFDLYNAYLAYKAFYRE 458
               SCOP domains d1y7ea2 A:4-100,A:234-458 Probable aminopeptidase ApeA                                           d1y7ea1 A:101-233 Probable aminopeptidase ApeA                                                                                       d1y7ea2 A:4-100,A:234-458 Probable aminopeptidase ApeA                                                                                                                                                                            SCOP domains
               CATH domains 1y7eA01 A:4-99,A:238-458 Zn peptidases                                                          1y7eA02 A:100-237 Aminopeptidase i, Domain 2                                                                                              1y7eA01 A:4-99,A:238-458 Zn peptidases                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------Peptidase_M18-1y7eA01 A:28-456                                                                                                                                                                                                                                                                                                                                                                                                               -- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...ee...........eee..........ee....hhhhh.ee.................eee..eeee........hhhhhh...eeeeeeee.....eeeeee...............--------------------...eeee.........hhhhhhhhhhhhhhhh.........eeeeee....eee.....eeee.hhhhhhhhhhhhhhhh.........ee.........--------..hhhhhhhhhhhhhhh.....hhhhhhhhhhheeee...ee....-------..........eeeeee.-----------hhhhhhhhhhhhhhhh..eeeeee..-----hhhhhhhhhhhh.eeeee..ee.......eeeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y7e A   4 QNPWIYLNEEEKNQILNFSESYKKFISKFKTEREVTAYALDKAKKLGFINAEEKKNLmPGDKIFYTCREKSVAFAIIGKNPIEDGmNFIVSHTDSPRLDAKPSPISEENELTFIKTNYYGGIKKYQWLSTPLSIRGVVFLKNGEKVEINIGDNENDPVFVIPDIL--------------------NLKILIGSLPIETKEKNKVKLATLQLIKEKYKIEEEDFVSSEIEIVPAGTAKDVGFDKALIGAYGQDDKICVFTSLESIFDLEETPNKTAICFLVDKEEI--------DSRYLEYFVSDmIFKIKKSEYNNLHVQKALWNSKSISADVCAAINP-------EQNAPQLGYGIPImKYT-----------DAELVSYIRQLLNKNNIAWQVATLGK-----GGTVAKFLAGYGIRTIDmGPAVISmHSPmEITSKFDLYNAYLAYKAFYRE 458
                                    13        23        33        43        53       |63        73        83     |  93       103       113       123       133       143       153       163    |    -         -     | 193       203       213       223       233       243       253       263       273       283    |    -   |   303    |  313       323       333        |-      |353       363  |      -    |  383       393       403     | 413       423  |    433   |   443       453     
                                                                                    61-MSE                      89-MSE                                                                        168                  189                                                                                                288      297        308-MSE                           342     350          363-MSE        378                      403   409              426-MSE  |   |                     
                                                                                                                                                                                                                                                                                                                                                                                                    366                                                                433-MSE                     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           437-MSE                 


Chain A from PDB  Type:PROTEIN  Length:404
 aligned with APEA_BORBZ | B7J1T9 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:455
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453     
           APEA_BORBZ     4 QNPWIYLNEEEKNQILNFSESYKKFISKFKTEREVTAYALDKAKKLGFINAEEKKNLMPGDKIFYTCREKSVAFAIIGKNPIEDGMNFIVSHTDSPRLDAKPSPISEENELTFIKTNYYGGIKKYQWLSTPLSIRGVVFLKNGEKVEINIGDNENDPVFVIPDILPHLDRKIQRNKKSDEIVEGENLKILIGSLPIETKEKNKVKLATLQLIKEKYKIEEEDFVSSEIEIVPAGTAKDVGFDKALIGAYGQDDKICVFTSLESIFDLEETPNKTAICFLVDKEEIGSTGSTGLDSRYLEYFVSDMIFKIKKSEYNNLHVQKALWNSKSISADVCAAINPLFSSVHDEQNAPQLGYGIPIMKYTGHGGKSMASDADAELVSYIRQLLNKNNIAWQVATLGKVEEGGGGTVAKFLAGYGIRTIDMGPAVISMHSPMEITSKFDLYNAYLAYKAFYRE 458
               SCOP domains d1y7ea2 A:4-100,A:234-458 Probable aminopeptidase ApeA                                           d1y7ea1 A:101-233 Probable aminopeptidase ApeA                                                                                       d1y7ea2 A:4-100,A:234-458 Probable aminopeptidase ApeA                                                                                                                                                                            SCOP domains
               CATH domains 1y7eA01 A:4-99,A:238-458 Zn peptidases                                                          1y7eA02 A:100-237 Aminopeptidase i, Domain 2                                                                                              1y7eA01 A:4-99,A:238-458 Zn peptidases                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------Peptidase_M18-1y7eA01 A:28-456                                                                                                                                                                                                                                                                                                                                                                                                               -- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...ee...........eee..........ee....hhhhh.ee.................eee..eeee........hhhhhh...eeeeeeee.....eeeeee...............--------------------...eeee.........hhhhhhhhhhhhhhhh.........eeeeee....eee.....eeee.hhhhhhhhhhhhhhhh.........ee.........--------..hhhhhhhhhhhhhhh.....hhhhhhhhhhheeee...ee....-------..........eeeeee.-----------hhhhhhhhhhhhhhhh..eeeeee..-----hhhhhhhhhhhh.eeeee..ee.......eeeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y7e A   4 QNPWIYLNEEEKNQILNFSESYKKFISKFKTEREVTAYALDKAKKLGFINAEEKKNLmPGDKIFYTCREKSVAFAIIGKNPIEDGmNFIVSHTDSPRLDAKPSPISEENELTFIKTNYYGGIKKYQWLSTPLSIRGVVFLKNGEKVEINIGDNENDPVFVIPDIL--------------------NLKILIGSLPIETKEKNKVKLATLQLIKEKYKIEEEDFVSSEIEIVPAGTAKDVGFDKALIGAYGQDDKICVFTSLESIFDLEETPNKTAICFLVDKEEI--------DSRYLEYFVSDmIFKIKKSEYNNLHVQKALWNSKSISADVCAAINP-------EQNAPQLGYGIPImKYT-----------DAELVSYIRQLLNKNNIAWQVATLGK-----GGTVAKFLAGYGIRTIDmGPAVISmHSPmEITSKFDLYNAYLAYKAFYRE 458
                                    13        23        33        43        53       |63        73        83     |  93       103       113       123       133       143       153       163    |    -         -     | 193       203       213       223       233       243       253       263       273       283    |    -   |   303    |  313       323       333        |-      |353       363  |      -    |  383       393       403     | 413       423  |    433   |   443       453     
                                                                                    61-MSE                      89-MSE                                                                        168                  189                                                                                                288      297        308-MSE                           342     350          363-MSE        378                      403   409              426-MSE  |   |                     
                                                                                                                                                                                                                                                                                                                                                                                                    366                                                                433-MSE                     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           437-MSE
   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, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Peptidase_MH (119)

(-) Gene Ontology  (7, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (APEA_BORBZ | B7J1T9)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    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: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.

Chain A   (APEA_BORBU | P0C925)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    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: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.

 Visualization

(-) Interactive Views

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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1y7e)
 
  Cis Peptide Bonds
    Asn A:341 - Pro A:342   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1y7e
    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
  APEA_BORBU | P0C925
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  APEA_BORBZ | B7J1T9
    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)
  3.4.11.-
    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

(-) Analysis Tools

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
  APEA_BORBU | P0C925
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  APEA_BORBZ | B7J1T9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1Y7E)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1Y7E)