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(-) Description

Title :  CRYSTAL STRUCTURE OF PEPTIDASE M16 INACTIVE DOMAIN FROM PSEUDOMONAS FLUORESCENS. NORTHEAST STRUCTURAL GENOMICS TARGET PLR293L
 
Authors :  J. Seetharaman, Y. Chen, F. Fang, R. Xiao, J. K. Everett, T. B. Acton, B. R G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomic Consortium (Nesg)
Date :  31 Mar 09  (Deposition) - 12 May 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Peptidase M16 Family, Pfl_5859, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Seetharaman, Y. Chen, F. Fang, R. Xiao, J. K. Everett, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J. F. Hunt
Crystal Structure Of Peptidase M16 Inactive Domain From Pseudomonas Fluorescens. Northeast Structural Genomics Target Plr293L
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDASE M16 INACTIVE DOMAIN FAMILY PROTEIN
    Atcc: BAA-477
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 53-479
    Gene: PFL_5859
    Organism Scientific: PSEUDOMONAS FLUORESCENS
    Organism Taxid: 220664
    Strain: PF-5

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 28)

Asymmetric/Biological Unit (1, 28)
No.NameCountTypeFull Name
1MSE28Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3GWB)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GWB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GWB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GWB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GWB)

(-) Exons   (0, 0)

(no "Exon" information available for 3GWB)

(-) 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:412
 aligned with Q4K4B6_PSEF5 | Q4K4B6 from UniProtKB/TrEMBL  Length:496

    Alignment length:415
                                    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       463       473     
         Q4K4B6_PSEF5    64 LNVQTWSTAEGAKVLFVEARELPMFDLRLIFAAGSSQDGNAPGVALLTNAMLNEGVAGKDVGAIAQGFEGLGADFGNGAYKDMAVASLRSLSAVDKREPALKLFAEVVGKPTFPADSLARIKNQMLAGFEYQKQNPGKLASLELMKRLYGTHPYAHASDGDAKSIPPITLAQLKAFHAKAYAAGNVVIALVGDLSRSDAEAIAAQVSAALPKGPALAKIEQPAEPKASIGHIEFPSSQTSLMLAQLGIDRDDPDYAAVSLGNQILGGGGFGTRLMSEVREKRGLTYGVYSGFTPMQARGPFMINLQTRAEMSEGTLKLVQDVFAEYLKNGPTQKELDDAKRELAGSFPLSTASNADIVGQLGAMGFYNLPLSYLEDFMRQSQELTVEQVKAAMNKHLNVDKMVIVSAGPTVAQKP 478
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeeeee.....eeeeeeee..hhhhh....hhhhhhhhhh..ee..eehhhhhhhhhh...eeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhh.................eeeeee....eeeeeeeee.......hhhhhhhhhhhhhh....hhhhhhhh........eeeee.......eeeeeeeee..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh---...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gwb A  12 LNVQTWSTAEGAKVLFVEARELPmFDLRLIFAAGSSQDGNAPGVALLTNAmLNEGVAGKDVGAIAQGFEGLGADFGNGAYKDmAVASLRSLSAVDKREPALKLFAEVVGKPTFPADSLARIKNQmLAGFEYQKQNPGKLASLELmKRLYGTHPYAHASDGDAKSIPPITLAQLKAFHAKAYAAGNVVIALVGDLSRSDAEAIAAQVSAALPKGPALAKIEQPAEPKASIGHIEFPSSQTSLmLAQLGIDRDDPDYAAVSLGNQILGGGGFGTRLmSEVREKRGLTYGVYSGFTPmQARGPFmINLQTRAEmSEGTLKLVQDVFAEYLKNGPTQKELDDAKRELAGS---STASNADIVGQLGAmGFYNLPLSYLEDFmRQSQELTVEQVKAAmNKHLNVDKmVIVSAGPTVAQKP 426
                                    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   |   381       391       401  |    411 |     421     
                                                  35-MSE                     62-MSE                          94-MSE                                   136-MSE             156-MSE                                                                                          253-MSE                          286-MSE             306-MSE  |      322-MSE                            357 361           375-MSE       389-MSE        404-MSE  413-MSE         
                                                                                                                                                                                                                                                                                                                                       313-MSE                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:412
 aligned with Q4K4B6_PSEF5 | Q4K4B6 from UniProtKB/TrEMBL  Length:496

    Alignment length:417
                                    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       463       473       
         Q4K4B6_PSEF5    64 LNVQTWSTAEGAKVLFVEARELPMFDLRLIFAAGSSQDGNAPGVALLTNAMLNEGVAGKDVGAIAQGFEGLGADFGNGAYKDMAVASLRSLSAVDKREPALKLFAEVVGKPTFPADSLARIKNQMLAGFEYQKQNPGKLASLELMKRLYGTHPYAHASDGDAKSIPPITLAQLKAFHAKAYAAGNVVIALVGDLSRSDAEAIAAQVSAALPKGPALAKIEQPAEPKASIGHIEFPSSQTSLMLAQLGIDRDDPDYAAVSLGNQILGGGGFGTRLMSEVREKRGLTYGVYSGFTPMQARGPFMINLQTRAEMSEGTLKLVQDVFAEYLKNGPTQKELDDAKRELAGSFPLSTASNADIVGQLGAMGFYNLPLSYLEDFMRQSQELTVEQVKAAMNKHLNVDKMVIVSAGPTVAQKPLP 480
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeeeee.....eeeeeeee..hhhhh....hhhhhhhhhh..ee..eehhhhhhhhhhh..eeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhh.................eeeeee....eeeeeeeee.......hhhhhhhhhhhhhh....hhhhhhhh........eeeee.......eeeeeeeee..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.-----.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gwb B  12 LNVQTWSTAEGAKVLFVEARELPmFDLRLIFAAGSSQDGNAPGVALLTNAmLNEGVAGKDVGAIAQGFEGLGADFGNGAYKDmAVASLRSLSAVDKREPALKLFAEVVGKPTFPADSLARIKNQmLAGFEYQKQNPGKLASLELmKRLYGTHPYAHASDGDAKSIPPITLAQLKAFHAKAYAAGNVVIALVGDLSRSDAEAIAAQVSAALPKGPALAKIEQPAEPKASIGHIEFPSSQTSLmLAQLGIDRDDPDYAAVSLGNQILGGGGFGTRLmSEVREKRGLTYGVYSGFTPmQARGPFmINLQTRAEmSEGTLKLVQDVFAEYLKNGPTQKELDDAKRELAGS-----ASNADIVGQLGAmGFYNLPLSYLEDFmRQSQELTVEQVKAAmNKHLNVDKmVIVSAGPTVAQKPLE 428
                                    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     |   - |     371   |   381       391       401  |    411 |     421       
                                                  35-MSE                     62-MSE                          94-MSE                                   136-MSE             156-MSE                                                                                          253-MSE                          286-MSE             306-MSE  |      322-MSE                            357   363         375-MSE       389-MSE        404-MSE  413-MSE           
                                                                                                                                                                                                                                                                                                                                       313-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  (0, 0)

(no "SCOP Domain" information available for 3GWB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GWB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GWB)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q4K4B6_PSEF5 | Q4K4B6)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain 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.
biological process
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.

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