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(-) Description

Title :  CRYSTAL STRUCTURE OF A NLPC/P60 FAMILY PROTEIN (BCE_2878) FROM BACILLUS CEREUS ATCC 10987 AT 1.79 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  17 Apr 09  (Deposition) - 05 May 09  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A
Keywords :  Nlpc/P60 Family Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Xu, P. Abdubek, T. Astakhova, H. L. Axelrod, C. Bakolitsa, X. Cai, D. Carlton, C. Chen, H. J. Chiu, M. Chiu, T. Clayton, D. Das, M. C. Deller L. Duan, K. Ellrott, C. L. Farr, J. Feuerhelm, J. C. Grant, A. Grzechnik G. W. Han, L. Jaroszewski, K. K. Jin, H. E. Klock, M. W. Knuth, P. Kozbial S. S. Krishna, A. Kumar, W. W. Lam, D. Marciano, M. D. Miller, A. T. Morse E. Nigoghossian, A. Nopakun, L. Okach, C. Puckett, R. Reyes, H. J. Tien C. B. Trame, H. Van Den Bedem, D. Weekes, T. Wooten, A. Yeh, K. O. Hodgson, J. Wooley, M. A. Elsliger, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Structure Of The Gamma-D-Glutamyl-L-Diamino Acid Endopeptidase Ykfc From Bacillus Cereus In Complex With L-Ala-[Gamma]-D-Glu: Insights Into Substrate Recognition By Nlpc/P60 Cysteine Peptidases
Acta Crystallogr. , Sect. F V. 66 1354 2010
PubMed-ID: 20944232  |  Reference-DOI: 10.1107/S1744309110021214

(-) Compounds

Molecule 1 - NLP/P60 FAMILY PROTEIN
    Atcc: 10987
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BCE_2878, NP_979181.1
    Organism Scientific: BACILLUS CEREUS ATCC 10987
    Organism Taxid: 222523

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 15)

Asymmetric/Biological Unit (6, 15)
No.NameCountTypeFull Name
1ALA1Mod. Amino AcidALANINE
2DGL1Ligand/IonD-GLUTAMIC ACID
3MSE5Mod. Amino AcidSELENOMETHIONINE
4OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
5PG46Ligand/IonTETRAETHYLENE GLYCOL
6PO41Ligand/IonPHOSPHATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:83 , TYR A:118 , TRP A:228 , ASP A:237 , ASP A:256 , DGL A:502 , HOH A:583BINDING SITE FOR RESIDUE ALA A 501
2AC2SOFTWARETRP A:228 , ASP A:237 , OCS A:238 , SER A:239 , ASP A:256 , SER A:257 , HIS A:290 , ALA A:501 , HOH A:555 , HOH A:722BINDING SITE FOR RESIDUE DGL A 502
3AC3SOFTWARESER A:156 , GLU A:157 , LYS A:158 , LYS A:160 , GLN A:188 , HOH A:609 , HOH A:620BINDING SITE FOR RESIDUE PO4 A 1
4AC4SOFTWAREILE A:215 , ASN A:216 , LYS A:219 , ILE A:296BINDING SITE FOR RESIDUE PG4 A 2
5AC5SOFTWARELEU A:47 , THR A:56 , ASP A:100 , LYS A:125 , HOH A:541 , HOH A:702BINDING SITE FOR RESIDUE PG4 A 3
6AC6SOFTWAREASP A:34 , ILE A:153 , PRO A:185 , ASN A:186 , HOH A:511 , HOH A:603BINDING SITE FOR RESIDUE PG4 A 4
7AC7SOFTWARETHR A:208 , ALA A:210 , GLY A:258 , ARG A:262 , SER A:288 , HOH A:622BINDING SITE FOR RESIDUE PG4 A 5
8AC8SOFTWAREASN A:154 , SER A:174 , ASP A:176 , ILE A:178 , SER A:179 , TRP A:191 , HOH A:569BINDING SITE FOR RESIDUE PG4 A 6
9AC9SOFTWAREMSE A:68 , THR A:69 , LEU A:70 , LYS A:73 , ALA A:307 , GLU A:308 , ARG A:309 , SER A:310 , HOH A:559BINDING SITE FOR RESIDUE PG4 A 7

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H41)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:57 -Pro A:58
2Asn A:154 -Pro A:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H41)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H41)

(-) Exons   (0, 0)

(no "Exon" information available for 3H41)

(-) 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:306
 aligned with Q736M3_BACC1 | Q736M3 from UniProtKB/TrEMBL  Length:333

    Alignment length:306
                                                                                                                                                                                                                                                                                                                                          333 
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328    | 
         Q736M3_BACC1    29 SKAFIDVSAATLWTAPDSLRPIDVPSATNPVDLWKWTKSMTLDEKLWLTNANKLETQALLGQEVTVVDKKGDWVKVLVHGQPTPRNEEGYPGWMPEKQLTYNQEFADKTNEPFVLVTKPTAILYINPSEKHKSLEVSYNTRLPLLSEDTISYRVLLPNGQKAWLRKNDGTFYRSQNDIPTPAADDLINTGKMFLGLPYIWAGTSGFGFDCSGFTHTIYKSHGITIPRDSGPQSRNGVAVDKEHLQKGDLIFFAHDQGKGSVHHVAMYIGDGNMIHSPRAERSVEIIPLNTPGYIEEYAGARRYLP-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee...eeeee......hhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..eeeeee...eeeeeeee..eeeeee...........eeeeee...ee.hhhhhhh....eeee...eeeeee.......eeeee...eeeeeee...eeeee.....eeeee...eeee.hhhhh...hhhhhhhhhhh..........ee..eehhhhhhhhhhhh.......hhhhhh...eeehhhhh....eeeeehhhhh..eeeeeeeee..eeee........eeee....hhhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3h41 A  29 SKAFIDVSAATLWTAPDSLRPIDVPSATNPVDLWKWTKSmTLDEKLWLTNANKLETQALLGQEVTVVDKKGDWVKVLVHGQPTPRNEEGYPGWmPEKQLTYNQEFADKTNEPFVLVTKPTAILYINPSEKHKSLEVSYNTRLPLLSEDTISYRVLLPNGQKAWLRKNDGTFYRSQNDIPTPAADDLINTGKmFLGLPYIWAGTSGFGFDcSGFTHTIYKSHGITIPRDSGPQSRNGVAVDKEHLQKGDLIFFAHDQGKGSVHHVAmYIGDGNmIHSPRAERSVEIIPLNTPGYIEEYAGARRYLPA 501
                                    38        48        58        68        78        88        98       108       118   |   128       138       148       158       168       178       188       198       208       218 |     228       238       248       258       268       278       288     | 298  |    308       318       328    ||
                                                                  68-MSE                                               122-MSE                                                                                           220-MSE           238-OCS                                                 294-MSE  |                             333|
                                                                                                                                                                                                                                                                                                          301-MSE                          501
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  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 3H41)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H41)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H41)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3H41)

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  3h41
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