Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS SUBTILIS YXEP PROTEIN (APC1829), A DINUCLEAR METAL BINDING PEPTIDASE FROM M20 FAMILY
 
Authors :  G. Minasov, L. Shuvalova, J. S. Brunzelle, F. R. Collart, W. F. Anderson Center For Structural Genomics (Mcsg)
Date :  08 Feb 05  (Deposition) - 22 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  M20 Family Peptidase, Dinuclear Metal Binding, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, L. Shuvalova, J. S. Brunzelle, F. R. Collart, W. F. Anderso
Structure Of Bacillus Subtilis Yxep Protein, A Dinuclear Metal Binding Peptidase From M20 Family
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN YXEP
    Chains: A, B
    EC Number: 3.5.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YXEP
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 20)

Asymmetric/Biological Unit (2, 20)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2NI4Ligand/IonNICKEL (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:98 , HIS A:100 , GLU A:133 , GLU A:134 , HIS A:158 , NI A:382 , HOH A:383 , HOH A:489BINDING SITE FOR RESIDUE NI A 381
2AC2SOFTWARECYS A:98 , GLU A:134 , HIS A:350 , NI A:381 , HOH A:383 , HOH A:385BINDING SITE FOR RESIDUE NI A 382
3AC3SOFTWARECYS B:98 , HIS B:100 , GLU B:133 , GLU B:134 , HIS B:158 , NI B:382 , HOH B:383 , HOH B:493BINDING SITE FOR RESIDUE NI B 381
4AC4SOFTWARECYS B:98 , GLU B:134 , HIS B:350 , NI B:381 , HOH B:383 , HOH B:386BINDING SITE FOR RESIDUE NI B 382

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YSJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YSJ)

(-) Sequences/Alignments

Asymmetric/Biological 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:359
 aligned with YXEP_BACSU | P54955 from UniProtKB/Swiss-Prot  Length:380

    Alignment length:378
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371        
           YXEP_BACSU     2 ADKAFHTRLINMRRDLHEHPELSFQEVETTKKIRRWLEEEQIEILDVPQLKTGVIAEIKGREDGPVIAIRADIDALPIQEQTNLPFASKVDGTMHACGHDFHTASIIGTAMLLNQRRAELKGTVRFIFQPAEEIAAGARKVLEAGVLNGVSAIFGMHNKPDLPVGTIGVKEGPLMASVDRFEIVIKGKGGHAGIPNNSIDPIAAAGQIISGLQSVVSRNISSLQNAVVSITRVQAGTSWNVIPDQAEMEGTVRTFQKEARQAVPEHMRRVAEGIAAGYGAQAEFKWFPYLPSVQNDGTFLNAASEAAARLGYQTVHAEQSPGGEDFALYQEKIPGFFVWMGTNGTEEWHHPAFTLDEEALTVASQYFAELAVIVLETI 379
               SCOP domains --d1ysja1 A:4-177,A:293-379 Protein YxeP                                                                                                                                        d1ysja2 A:17        8-292 Protein Yxe           P                                                                  d1ysja1 A:4-177,A:293-379 Protein YxeP                                                  SCOP domains
               CATH domains 1ysjA01 A:2-174,A:291-379 Zn peptidases                                                                                                                                      ---1ysjA02 A:17        8-290  [code=3.30           .70.360, no name defined]                                        1ysjA01 A:2-174,A:291-379 Zn peptidases                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..ee.........eeeeee......eeeeeee.........................hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhhh.....eeeeeeeeee......eeee..eeee..eeeeeeeee..--------...hhhhhhhhhhhhhh-----------..eeeeeeeee.........eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee..eeehhhhhhhhhhhhhhh..eeee........hhhhhhh...eeeeeee................hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ysj A   2 ADKAFHTRLINmRRDLHEHPELSFQEVETTKKIRRWLEEEQIEILDVPQLKTGVIAEIKGREDGPVIAIRADIDALPIQEQTNLPFASKVDGTmHACGHDFHTASIIGTAmLLNQRRAELKGTVRFIFQPAEEIAAGARKVLEAGVLNGVSAIFGmHNKPDLPVGTIGVKEGPLmASVDRFEIVIKGK--------NSIDPIAAAGQIISGLQ-----------NAVVSITRVQAGTSWNVIPDQAEmEGTVRTFQKEARQAVPEHmRRVAEGIAAGYGAQAEFKWFPYLPSVQNDGTFLNAASEAAARLGYQTVHAEQSPGGEDFALYQEKIPGFFVWmGTNGTEEWHHPAFTLDEEALTVASQYFAELAVIVLETI 379
                                    11 |      21        31        41        51        61        71        81        91   |   101       111|      121       131       141       151     | 161       171    |  181       | -      |201       211  |      -    |  231       241       251       261      |271       281       291       301       311       321       331       341       351       361       371        
                                      13-MSE                                                                            95-MSE          112-MSE                                      157-MSE            176-MSE      189      198             214         226                    249-MSE            268-MSE                                                                  341-MSE                                  


Chain B from PDB  Type:PROTEIN  Length:356
 aligned with YXEP_BACSU | P54955 from UniProtKB/Swiss-Prot  Length:380

    Alignment length:377
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       
           YXEP_BACSU     3 DKAFHTRLINMRRDLHEHPELSFQEVETTKKIRRWLEEEQIEILDVPQLKTGVIAEIKGREDGPVIAIRADIDALPIQEQTNLPFASKVDGTMHACGHDFHTASIIGTAMLLNQRRAELKGTVRFIFQPAEEIAAGARKVLEAGVLNGVSAIFGMHNKPDLPVGTIGVKEGPLMASVDRFEIVIKGKGGHAGIPNNSIDPIAAAGQIISGLQSVVSRNISSLQNAVVSITRVQAGTSWNVIPDQAEMEGTVRTFQKEARQAVPEHMRRVAEGIAAGYGAQAEFKWFPYLPSVQNDGTFLNAASEAAARLGYQTVHAEQSPGGEDFALYQEKIPGFFVWMGTNGTEEWHHPAFTLDEEALTVASQYFAELAVIVLETI 379
               SCOP domains d1ysjb1 B:3-177,B:293-379 Protein YxeP                                                                                                                                         d1ysjb2 B:17          8-292 Protein Y           xeP                                                                d1ysjb1 B:3-177,B:293-379 Protein YxeP                                                  SCOP domains
               CATH domains 1ysjB01 B:3-174,B:291-379 Zn peptidases                                                                                                                                     ---1ysjB02 B:17          8-290  [code=3.           30.70.360, no name defined]                                      1ysjB01 B:3-174,B:291-379 Zn peptidases                                                   CATH domains
           Pfam domains (1) ------------------------------------------------------------------Peptidase_M20-1ysjB01 B:69-373                                                                                                                                                                                                                                                                                   ------ Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------Peptidase_M20-1ysjB02 B:69-373                                                                                                                                                                                                                                                                                   ------ Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------M20_dimer-1y          sjB03 B:178-280                                                                  --------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------M20_dimer-1y          sjB04 B:178-280                                                                  --------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh...ee.........eeeeee..eeeeeeeeeee.........................hhhhhhhhhhhhhhhhh......eeeeeeeee......hhhhhhhhh.....eeeeeeeeee......eeee..eeee.eeeeeeeeeee.----------.hhhhhhhhhhhh..-----------..eeeeeeeee.........eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee..eeehhhhhhhhhhhhhh...eeee........hhhhhhh...eeeeeee................hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ysj B   3 DKAFHTRLINmRRDLHEHPELSFQEVETTKKIRRWLEEEQIEILDVPQLKTGVIAEIKGREDGPVIAIRADIDALPIQEQTNLPFASKVDGTmHACGHDFHTASIIGTAmLLNQRRAELKGTVRFIFQPAEEIAAGARKVLEAGVLNGVSAIFGmHNKPDLPVGTIGVKEGPLmASVDRFEIVIKGK----------IDPIAAAGQIISGLQ-----------NAVVSITRVQAGTSWNVIPDQAEmEGTVRTFQKEARQAVPEHmRRVAEGIAAGYGAQAEFKWFPYLPSVQNDGTFLNAASEAAARLGYQTVHAEQSPGGEDFALYQEKIPGFFVWmGTNGTEEWHHPAFTLDEEALTVASQYFAELAVIVLETI 379
                                    12|       22        32        42        52        62        72        82        92  |    102       112       122       132       142       152    |  162       172   |   182      |  -       202       212 |       -   |   232       242      |252       262     | 272       282       292       302       312       322       332       342       352       362       372       
                                     13-MSE                                                                            95-MSE          112-MSE                                      157-MSE            176-MSE      189        200           214         226                    249-MSE            268-MSE                                                                  341-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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_MH (119)
(-)
Clan: no clan defined [family: M20_dimer] (13)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (YXEP_BACSU | P54955)
molecular function
    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.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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 ]
    NI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ysj)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  1ysj
    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
  YXEP_BACSU | P54955
    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)
  3.5.1.14
    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
  YXEP_BACSU | P54955
    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 1YSJ)

(-) Related Entries Specified in the PDB File

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