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(-) Description

Title :  YKUD L,D-TRANSPEPTIDASE
 
Authors :  M. Blaise, S. Fuglsang Midtgaard, S. Roi Midtgaard, T. Boesen, S. Thi
Date :  15 Sep 11  (Deposition) - 26 Sep 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Peptidoglycan Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Blaise, S. Fuglsang Midtgaard, S. Roi Midtgaard, T. Boesen, S. Thirup
Structures Of Three New Crystal Forms Of The Ykud L, D-Transpeptidase From B. Subtilis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE L, D-TRANSPEPTIDASE YKUD
    ChainsA
    EC Number2.-.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VectorPGS21A
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    SynonymYKUD L,D TRANSPEPTIDASE, SPORE PROTEIN YKUD

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CME1Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:136 , LYS A:137 , GLY A:138 , CME A:139 , ARG A:141 , HOH A:2188BINDING SITE FOR RESIDUE SO4 A1165

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A1K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4A1K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A1K)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LYSMPS51782 LysM domain profile.YKUD_BACSU2-45  1A:2-45
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LYSMPS51782 LysM domain profile.YKUD_BACSU2-45  2A:2-45

(-) Exons   (0, 0)

(no "Exon" information available for 4A1K)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:165
 aligned with YKUD_BACSU | O34816 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:165
                             1                                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159     
           YKUD_BACSU     - -MLTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPGLPDPYTIPYHIAVSIGAKTLTLSLNNRVMKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSKQHYGIHGTNNPASIGKAVSKGCIRMHNKDVIELASIVPNGTRVTINR 164
               SCOP domains d4a1ka1 A:0-48 automated matches                 d4a1ka2 A:49-164 automated matches                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhh..hhhhhhhhhhhhhhh.....eeee....hhhhh.eeeeee....eeeeee..eeeeeee..ee.hhhh...eeeeeeeeee..hhhhh.eeeee.....eee...hhhhh..eee...ee.hhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --LYSM  PDB: A:2-45 UniProt: 2-45             ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a1k A   0 GMLTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPGLPDPYTIPYHIAVSIGAKTLTLSLNNRVMKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSAAHYGIHGTNNPASIGKAVSKGcIRMHNKDVIELASIVPNGTRVTINR 164
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159     
                                                                                                                                                                     139-CME                     

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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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A1K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A1K)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (YKUD_BACSU | O34816)
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.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
    GO:0031160    spore wall    The specialized envelope lying outside the cell membrane of a spore.

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 Related Entries

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

UniProtKB/Swiss-Prot
        YKUD_BACSU | O348161y7m 2mtz 3zqd 4a1i 4a1j 4a52

(-) Related Entries Specified in the PDB File

1y7m CRYSTAL STRUCTURE OF THE B. SUBTILIS YKUD PROTEIN AT 2 ARESOLUTION
3zqd B. SUBTILIS L,D-TRANSPEPTIDASE
4a1i YKUD FROM B.SUBTILIS
4a1j YKUD L,D-TRANSPEPTIDASE FROM B.SUBTILIS