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(-) Description

Title :  CRYSTAL STRUCTURE OF THE B. SUBTILIS YKUD PROTEIN AT 2 A RESOLUTION
 
Authors :  J. A. Bielnicki, Y. Devedjiev, U. Derewenda, Z. Dauter, A. Joachimiak, Z. S. Derewenda, Midwest Center For Structural Genomics (Mcsg)
Date :  09 Dec 04  (Deposition) - 01 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Surface Mutagenesis, Cysteine Proteases, Cell Wall Catabolism, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Bielnicki, Y. Devedjiev, U. Derewenda, Z. Dauter, A. Joachimiak, Z. S. Derewenda
B. Subtilis Ykud Protein At 2. 0 A Resolution: Insights Into The Structure And Function Of A Novel, Ubiquitous Family Of Bacterial Enzymes.
Proteins V. 62 144 2006
PubMed-ID: 16287140  |  Reference-DOI: 10.1002/PROT.20702
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN BSU14040
    Chains: A, B
    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: YKUD
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
    Organism Taxid: 224308
    Strain: SUBSP. SUBTILIS STR. 168

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1CD2Ligand/IonCADMIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:139 , SO4 A:203 , HOH A:204 , HIS B:119BINDING SITE FOR RESIDUE CD A 201
2AC2SOFTWAREHIS A:119 , CYS B:139 , SO4 B:204 , HOH B:207BINDING SITE FOR RESIDUE CD B 202
3AC3SOFTWAREHIS A:123 , SER A:136 , LYS A:137 , GLY A:138 , CYS A:139 , ARG A:141 , CD A:201 , HIS B:119BINDING SITE FOR RESIDUE SO4 A 203
4AC4SOFTWAREHIS A:119 , HIS B:123 , SER B:136 , LYS B:137 , GLY B:138 , CYS B:139 , ARG B:141 , CD B:202BINDING SITE FOR RESIDUE SO4 B 204
5AC5SOFTWAREARG A:159 , HOH A:238 , TYR B:96 , ARG B:159BINDING SITE FOR RESIDUE SO4 B 205
6AC6SOFTWAREASN A:144 , LYS B:145 , HOH B:211 , HOH B:225BINDING SITE FOR RESIDUE SO4 B 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y7M)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala B:25 -Leu B:26

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y7M)

(-) PROSITE Motifs  (1, 2)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1Y7M)

(-) 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:164
 aligned with YKUD_BACSU | O34816 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
           YKUD_BACSU     1 MLTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPGLPDPYTIPYHIAVSIGAKTLTLSLNNRVMKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSKQHYGIHGTNNPASIGKAVSKGCIRMHNKDVIELASIVPNGTRVTINR 164
               SCOP domains d1y7ma2 A:1-48                                  d1y7ma1 A:49-164 Hypothetical protein YkuD, C-terminal domain                                                        SCOP domains
               CATH domains -1y7mA01 A:2-47                                1y7mA02 A:48-164 L,D-transpeptidase catalytic domain-like                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhh......................eeee....hhhhh.eeeeee....eeeeee..eeeeeee..ee........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
                 1y7m A   1 mLTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPGLPDPYTIPYHIAVSIGAKTLTLSLNNRVmKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSAAHYGIHGTNNPASIGKAVSKGCIRmHNKDVIELASIVPNGTRVTINR 164
                            |       10        20        30        40        50        60        70     |  80        90       100       110       120       130       140 |     150       160    
                            |                                                                         76-MSE                                                           142-MSE                  
                            1-MSE                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:164
 aligned with YKUD_BACSU | O34816 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
           YKUD_BACSU     1 MLTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPGLPDPYTIPYHIAVSIGAKTLTLSLNNRVMKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSKQHYGIHGTNNPASIGKAVSKGCIRMHNKDVIELASIVPNGTRVTINR 164
               SCOP domains d1y7mb2 B:1-48                                  d1y7mb1 B:49-164 Hypothetical protein YkuD, C-terminal domain                                                        SCOP domains
               CATH domains -1y7mB01 B:2-47                                1y7mB02 B:48-164 L,D-transpeptidase catalytic domain-like                                                             CATH domains
           Pfam domains (1) ---LysM-1y7mB01 B:4-46                        --------YkuD-1y7mB03 B:55-162                                                                                       -- Pfam domains (1)
           Pfam domains (2) ---LysM-1y7mB02 B:4-46                        --------YkuD-1y7mB04 B:55-162                                                                                       -- Pfam domains (2)
         Sec.struct. author .eeee.....hhhhhhhhh......................eeee....hhhhh.eeeeee....eeeeee..eeeeeee..ee........eeeeeeeeee..hhhhh.eeeee.....eee...hhhhh..eee...ee.hhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -LYSM  PDB: B:2-45 UniProt: 2-45             ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y7m B   1 mLTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPGLPDPYTIPYHIAVSIGAKTLTLSLNNRVmKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSAAHYGIHGTNNPASIGKAVSKGCIRmHNKDVIELASIVPNGTRVTINR 164
                            |       10        20        30        40        50        60        70     |  80        90       100       110       120       130       140 |     150       160    
                            1-MSE                                                                     76-MSE                                                           142-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: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: LysM (1)
(-)
Clan: YkuD (2)
(-)
Family: YkuD (2)
(-)
Bacillus subtilis (1)
2aYkuD-1y7mB03B:55-162
2bYkuD-1y7mB04B:55-162

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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 | O34816: 2mtz 3zqd 4a1i 4a1j 4a1k 4a52

(-) Related Entries Specified in the PDB File

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