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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS PBP4A, AND ITS COMPLEX WITH A PEPTIDOGLYCAN MIMETIC PEPTIDE.
 
Authors :  E. Sauvage, R. Herman, F. Kerff, C. Duez, P. Charlier
Date :  15 Nov 06  (Deposition) - 03 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  D-Ala-D-Ala- Carboxypeptidase, Peptidoglycan Synthesis, Penicillin-Binding Protein, Peptidoglycan, Cell Division, Bacillus Subtilis, Cell Wall, Hydrolase, Cell Shape, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Sauvage, C. Duez, R. Herman, F. Kerff, S. Petrella, J. W. Anderson, S. A. Adediran, R. F. Pratt, J. M. Frere, P. Charlier
Crystal Structure Of The Bacillus Subtilis Penicillin-Binding Protein 4A, And Its Complex With A Peptidoglycan Mimetic Peptide.
J. Mol. Biol. V. 371 528 2007
PubMed-ID: 17582436  |  Reference-DOI: 10.1016/J.JMB.2007.05.071

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN
    Chains: A, B
    Fragment: RESIDUES 30-491
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1DAL2Ligand/IonD-ALANINE
2REZ2Ligand/Ion(2R)-2-AMINO-7-{[(1R)-1-CARBOXYETHYL]AMINO}-7-OXOHEPTANOIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1DAL1Ligand/IonD-ALANINE
2REZ1Ligand/Ion(2R)-2-AMINO-7-{[(1R)-1-CARBOXYETHYL]AMINO}-7-OXOHEPTANOIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1DAL1Ligand/IonD-ALANINE
2REZ1Ligand/Ion(2R)-2-AMINO-7-{[(1R)-1-CARBOXYETHYL]AMINO}-7-OXOHEPTANOIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:51 , SER A:52 , PRO A:142 , ASP A:145 , TYR A:150 , ASN A:301 , SER A:348 , ILE A:350 , HIS A:352 , GLY A:413 , SER A:414 , LEU A:415 , SER A:416 , DAL A:501BINDING SITE FOR RESIDUE REZ A 500
2AC2SOFTWAREALA B:51 , SER B:52 , ASP B:145 , TYR B:150 , ASN B:301 , HIS B:352 , GLY B:413 , SER B:414 , LEU B:415 , SER B:416 , DAL B:501BINDING SITE FOR RESIDUE REZ B 500
3AC3SOFTWARESER B:52 , SER B:299 , LYS B:411 , THR B:412 , GLY B:413 , SER B:414 , REZ B:500BINDING SITE FOR RESIDUE DAL B 501
4AC4SOFTWARESER A:52 , SER A:299 , LYS A:411 , THR A:412 , GLY A:413 , REZ A:500BINDING SITE FOR RESIDUE DAL A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J9P)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:189 -Pro A:190
2Ser B:189 -Pro B:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J9P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J9P)

(-) Exons   (0, 0)

(no "Exon" information available for 2J9P)

(-) Sequences/Alignments

Asymmetric 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:458
 aligned with DACC_BACSU | P39844 from UniProtKB/Swiss-Prot  Length:491

    Alignment length:458
                                    43        53        63        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       483        
           DACC_BACSU    34 DALSGQIDKILADHPALEGAMAGITVRSAETGAVLYEHSGDTRMRPASSLKLLTAAAALSVLGENYSFTTEVRTDGTLKGKKLNGNLYLKGKGDPTLLPSDFDKMAEILKHSGVKVIKGNLIGDDTWHDDMRLSPDMPWSDEYTYYGAPISALTASPNEDYDAGTVIVEVTPNQKEGEEPAVSVSPKTDYITIKNDAKTTAAGSEKDLTIEREHGTNTITIEGSVPVDANKTKEWISVWEPAGYALDLFKQSLKKQGITVKGDIKTGEAPSSSDVLLSHRSMPLSKLFVPFMKLSNNGHAEVLVKEMGKVKKGEGSWEKGLEVLNSTLPEFGVDSKSLVLRDGSGISHIDAVSSDQLSQLLYDIQDQSWFSAYLNSLPVAGNPDRMVGGTLRNRMKGTPAQGKVRAKTGSLSTVSSLSGYAETKSGKKLVFSILLNGLIDEEDGKDIEDQIAVILANQ 491
               SCOP domains d2j9pa1 A:5-462 Penicillin-binding protein DacC                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2j9pA01 A:5-71,A:286-462 DD-peptidase/beta-lactamase superfamily   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2j9pA01 A:5-71,A:286-462 DD-peptidase/beta-lactamase superfamily                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeee.......hhhhhhhhhhhhhhhhh......eeeeee.......ee...eeeeee.......hhhhhhhhhhhh....ee...eeee.............hhhhh......................eeeeeee.........eeeee......eeeeeeeee........eeee.....eeeeeeeee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eeee......eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhh..............hhhhhhhhhhhhhhh.hhhhhhhh...........hhhhh...........eeeeeeee..eeeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j9p A   5 DALSGQIDKILADHPALEGAMAGITVRSAETGAVLYEHSGDTRMRPASSLKLLTAAAALSVLGENYSFTTEVRTDGTLKGKKLNGNLYLKGKGDPTLLPSDFDKMAEILKHSGVKVIKGNLIGDDTWHDDMRLSPDMPWSDEYTYYGAPISALTASPNEDYDAGTVIVEVTPNQKEGEEPAVSVSPKTDYITIKNDAKTTAAGSEKDLTIEREHGTNTITIEGSVPVDANKTKEWISVWEPAGYALDLFKQSLKKQGITVKGDIKTGEAPSSSDVLLSHRSMPLSKLFVPFMKLSNNGHAEVLVKEMGKVKKGEGSWEKGLEVLNSTLPEFGVDSKSLVLRDGSGISHIDAVSSDQLSQLLYDIQDQSWFSAYLNSLPVAGNPDRMVGGTLRNRMKGTPAQGKVRAKTGSLSTVSSLSGYAETKSGKKLVFSILLNGLIDEEDGKDIEDQIAVILANQ 462
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454        


Chain B from PDB  Type:PROTEIN  Length:458
 aligned with DACC_BACSU | P39844 from UniProtKB/Swiss-Prot  Length:491

    Alignment length:458
                                    43        53        63        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       483        
           DACC_BACSU    34 DALSGQIDKILADHPALEGAMAGITVRSAETGAVLYEHSGDTRMRPASSLKLLTAAAALSVLGENYSFTTEVRTDGTLKGKKLNGNLYLKGKGDPTLLPSDFDKMAEILKHSGVKVIKGNLIGDDTWHDDMRLSPDMPWSDEYTYYGAPISALTASPNEDYDAGTVIVEVTPNQKEGEEPAVSVSPKTDYITIKNDAKTTAAGSEKDLTIEREHGTNTITIEGSVPVDANKTKEWISVWEPAGYALDLFKQSLKKQGITVKGDIKTGEAPSSSDVLLSHRSMPLSKLFVPFMKLSNNGHAEVLVKEMGKVKKGEGSWEKGLEVLNSTLPEFGVDSKSLVLRDGSGISHIDAVSSDQLSQLLYDIQDQSWFSAYLNSLPVAGNPDRMVGGTLRNRMKGTPAQGKVRAKTGSLSTVSSLSGYAETKSGKKLVFSILLNGLIDEEDGKDIEDQIAVILANQ 491
               SCOP domains d2j9pb1 B:5-462 Penicillin-binding protein DacC                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2j9pB01 B:5-71,B:286-462 DD-peptidase/beta-lactamase superfamily   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2j9pB01 B:5-71,B:286-462 DD-peptidase/beta-lactamase superfamily                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeee.......hhhhhhhhhhhhhhh........eeeee.............eeeee......hhhhhhhhhhhhhhh...ee...eeee....................hhhh................eeeeeee.........eeeee......eeeeeeeee......eeeeee.....eeeeeeeee......eeeee..hhhhhhhhhhhhhhhhhh.ee...eee........eeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhh..............hhhhhhhhhhhhh...hhhhhhh........hhhhhhhhh...........eeeeeeee..eeeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j9p B   5 DALSGQIDKILADHPALEGAMAGITVRSAETGAVLYEHSGDTRMRPASSLKLLTAAAALSVLGENYSFTTEVRTDGTLKGKKLNGNLYLKGKGDPTLLPSDFDKMAEILKHSGVKVIKGNLIGDDTWHDDMRLSPDMPWSDEYTYYGAPISALTASPNEDYDAGTVIVEVTPNQKEGEEPAVSVSPKTDYITIKNDAKTTAAGSEKDLTIEREHGTNTITIEGSVPVDANKTKEWISVWEPAGYALDLFKQSLKKQGITVKGDIKTGEAPSSSDVLLSHRSMPLSKLFVPFMKLSNNGHAEVLVKEMGKVKKGEGSWEKGLEVLNSTLPEFGVDSKSLVLRDGSGISHIDAVSSDQLSQLLYDIQDQSWFSAYLNSLPVAGNPDRMVGGTLRNRMKGTPAQGKVRAKTGSLSTVSSLSGYAETKSGKKLVFSILLNGLIDEEDGKDIEDQIAVILANQ 462
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454
   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  (1, 2)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J9P)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DACC_BACSU | P39844)
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:0009002    serine-type D-Ala-D-Ala carboxypeptidase activity    Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
    GO:0004185    serine-type carboxypeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  2j9p
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  DACC_BACSU | P39844
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 Related Entries

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

UniProtKB/Swiss-Prot
        DACC_BACSU | P39844: 1w5d

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2J9P)