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(-) Description

Title :  MEPA, INACTIVE FORM WITHOUT ZN IN P21
 
Authors :  M. Marcyjaniak, S. G. Odintsov, I. Sabala, M. Bochtler
Date :  11 Jul 04  (Deposition) - 07 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Las Enzyme, Metallopeptidase, Peptidoglycan Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Marcyjaniak, S. G. Odintsov, I. Sabala, M. Bochtler
Peptidoglycan Amidase Mepa Is A Las Metallopeptidase
J. Biol. Chem. V. 279 43982 2004
PubMed-ID: 15292190  |  Reference-DOI: 10.1074/JBC.M406735200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PENICILLIN-INSENSITIVE MUREIN ENDOPEPTIDASE
    Chains: A, B
    EC Number: 3.4.99.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MEPA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: D-ALANYL-D-ALANINE-ENDOPEPTIDASE, DD- ENDOPEPTIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1BU11Ligand/Ion1,4-BUTANEDIOL
2SO49Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:205 , HIS A:206 , ARG A:207 , ALA A:208 , HIS A:209 , HOH A:695BINDING SITE FOR RESIDUE SO4 A 561
02AC2SOFTWAREGLN B:205 , HIS B:206 , ARG B:207 , ALA B:208 , HIS B:209 , HOH B:603 , HOH B:662 , HOH B:718BINDING SITE FOR RESIDUE SO4 B 562
03AC3SOFTWAREASN A:179 , PHE A:204 , GLN A:205 , ARG A:207 , HOH A:716BINDING SITE FOR RESIDUE SO4 A 563
04AC4SOFTWARELYS A:149 , HIS B:150 , VAL B:151 , VAL B:152 , SER B:153 , HOH B:741 , HOH B:805BINDING SITE FOR RESIDUE SO4 B 564
05AC5SOFTWARELEU A:136 , ARG A:137 , PRO A:230 , SER A:231 , HOH A:641BINDING SITE FOR RESIDUE SO4 A 565
06AC6SOFTWARESER B:55 , GLU B:56 , HIS B:57 , BU1 B:570 , HOH B:670 , HOH B:726 , HOH B:733BINDING SITE FOR RESIDUE SO4 B 566
07AC7SOFTWAREARG B:175 , ARG B:201 , PRO B:229 , HOH B:725BINDING SITE FOR RESIDUE SO4 B 567
08AC8SOFTWAREARG A:175 , ARG A:201 , HOH A:732BINDING SITE FOR RESIDUE SO4 A 568
09AC9SOFTWAREASN B:179 , PHE B:204 , GLN B:205 , ARG B:207BINDING SITE FOR RESIDUE SO4 B 569
10BC1SOFTWAREHIS A:150 , GLU B:56 , LYS B:149 , PHE B:243 , GLU B:244 , SO4 B:566BINDING SITE FOR RESIDUE BU1 B 570

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:44 -A:265
2A:187 -A:235
3A:216 -A:223
4B:44 -B:265
5B:187 -B:235
6B:216 -B:223

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TZP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TZP)

(-) Exons   (0, 0)

(no "Exon" information available for 1TZP)

(-) 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:240
 aligned with MEPA_ECOLI | P0C0T5 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:255
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269     
           MEPA_ECOLI    20 ATPWQKITQPVPGSAQSIGSFSNGCIVGADTLPIQSEHYQVMRTDQRRYFGHPDLVMFIQRLSSQVSNLGMGTVLIGDMGMPAGGRFNGGHASHQTGLDVDIFLQLPKTRWTSAQLLRPQALDLVSRDGKHVVSTLWKPEIFSLIKLAAQDKDVTRIFVNPAIKQQLCLDAGTDRDWLRKVRPWFQHRAHMHVRLRCPADSLECEDQPLPPSGDGCGAELQSWFEPPKPGTTKPEKKTPPPLPPSCQALLDEHVI 274
               SCOP domains d1tzpa_ A: D-alanyl-D-alanine-endopeptidase MepA                                                                                                                                                                                                                SCOP domains
               CATH domains 1tzpA00 A:20-274  [code=3.30.1380.10, no name defined]                                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh........eeeee..eeeee..ee.......eee.hhhhh..eehhhhhhhhhhhhhhhhhh....eee......................eeeee........hhhhhhh...................hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhh...hhhhh.eee......eeeeee.....................hhhhhhh..---------------..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tzp A  20 ATPWQKITQPVPGSAQSIGSFSNGCIVGADTLPIQSEHYQVMRTDQRRYFGHPDLVMFIQRLSSQVSNLGMGTVLIGDMGMPAGGRFNGGHASHQTGLDVDIFLQLPKTRWTSAQLLRPQALDLVSRDGKHVVSTLWKPEIFSLIKLAAQDKDVTRIFVNPAIKQQLCLDAGTDRDWLRKVRPWFQHRAHMHVRLRCPADSLECEDQPLPPSGDGCGAELQSWFE---------------PLPPSCQALLDEHVI 274
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239    |    -         -|      269     
                                                                                                                                                                                                                                                          244             260              


Chain A from PDB  Type:PROTEIN  Length:240
 aligned with MEPA_SHIFL | P0C0T6 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:255
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269     
           MEPA_SHIFL    20 ATPWQKITQPVPGSAQSIGSFSNGCIVGADTLPIQSEHYQVMRTDQRRYFGHPDLVMFIQRLSSQVSNLGMGTVLIGDMGMPAGGRFNGGHASHQTGLDVDIFLQLPKTRWTSAQLLRPQALDLVSRDGKHVVSTLWKPEIFSLIKLAAQDKDVTRIFVNPAIKQQLCLDAGTDRDWLRKVRPWFQHRAHMHVRLRCPADSLECEDQPLPPSGDGCGAELQSWFEPPKPGTTKPEKKTPPPLPPSCQALLDEHVI 274
               SCOP domains d1tzpa_ A: D-alanyl-D-alanine-endopeptidase MepA                                                                                                                                                                                                                SCOP domains
               CATH domains 1tzpA00 A:20-274  [code=3.30.1380.10, no name defined]                                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh........eeeee..eeeee..ee.......eee.hhhhh..eehhhhhhhhhhhhhhhhhh....eee......................eeeee........hhhhhhh...................hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhh...hhhhh.eee......eeeeee.....................hhhhhhh..---------------..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tzp A  20 ATPWQKITQPVPGSAQSIGSFSNGCIVGADTLPIQSEHYQVMRTDQRRYFGHPDLVMFIQRLSSQVSNLGMGTVLIGDMGMPAGGRFNGGHASHQTGLDVDIFLQLPKTRWTSAQLLRPQALDLVSRDGKHVVSTLWKPEIFSLIKLAAQDKDVTRIFVNPAIKQQLCLDAGTDRDWLRKVRPWFQHRAHMHVRLRCPADSLECEDQPLPPSGDGCGAELQSWFE---------------PLPPSCQALLDEHVI 274
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239    |    -         -|      269     
                                                                                                                                                                                                                                                          244             260              


Chain B from PDB  Type:PROTEIN  Length:236
 aligned with MEPA_ECOLI | P0C0T5 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:250
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272
           MEPA_ECOLI    23 WQKITQPVPGSAQSIGSFSNGCIVGADTLPIQSEHYQVMRTDQRRYFGHPDLVMFIQRLSSQVSNLGMGTVLIGDMGMPAGGRFNGGHASHQTGLDVDIFLQLPKTRWTSAQLLRPQALDLVSRDGKHVVSTLWKPEIFSLIKLAAQDKDVTRIFVNPAIKQQLCLDAGTDRDWLRKVRPWFQHRAHMHVRLRCPADSLECEDQPLPPSGDGCGAELQSWFEPPKPGTTKPEKKTPPPLPPSCQALLDEH 272
               SCOP domains d1tzpb_ B: D-alanyl-D-alanine-endopeptidase MepA                                                                                                                                                                                                           SCOP domains
               CATH domains 1tzpB00 B:23-272  [code=3.30.1380.10, no name defined]                                                                                                                                                                                                     CATH domains
           Pfam domains (1) ------------Peptidase_M74-1tzpB01 B:35-272                                                                                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) ------------Peptidase_M74-1tzpB02 B:35-272                                                                                                                                                                                                                 Pfam domains (2)
         Sec.struct. author ............eeeee..eeeee..ee.......eee.hhhhh..eehhhhhhhhhhhhhhhhhh....eee......................eeeee........hhhhhhh...................hhhhhhhhhhhhh...eeeeeehhhhhhhhhhhh...hhhhh.eee......eeeeee.....................hhhhhhh..--------------...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tzp B  23 WQKITQPVPGSAQSIGSFSNGCIVGADTLPIQSEHYQVMRTDQRRYFGHPDLVMFIQRLSSQVSNLGMGTVLIGDMGMPAGGRFNGGHASHQTGLDVDIFLQLPKTRWTSAQLLRPQALDLVSRDGKHVVSTLWKPEIFSLIKLAAQDKDVTRIFVNPAIKQQLCLDAGTDRDWLRKVRPWFQHRAHMHVRLRCPADSLECEDQPLPPSGDGCGAELQSWFE--------------PPLPPSCQALLDEH 272
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242 |       -      |262       272
                                                                                                                                                                                                                                                       244            259             


Chain B from PDB  Type:PROTEIN  Length:236
 aligned with MEPA_SHIFL | P0C0T6 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:250
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272
           MEPA_SHIFL    23 WQKITQPVPGSAQSIGSFSNGCIVGADTLPIQSEHYQVMRTDQRRYFGHPDLVMFIQRLSSQVSNLGMGTVLIGDMGMPAGGRFNGGHASHQTGLDVDIFLQLPKTRWTSAQLLRPQALDLVSRDGKHVVSTLWKPEIFSLIKLAAQDKDVTRIFVNPAIKQQLCLDAGTDRDWLRKVRPWFQHRAHMHVRLRCPADSLECEDQPLPPSGDGCGAELQSWFEPPKPGTTKPEKKTPPPLPPSCQALLDEH 272
               SCOP domains d1tzpb_ B: D-alanyl-D-alanine-endopeptidase MepA                                                                                                                                                                                                           SCOP domains
               CATH domains 1tzpB00 B:23-272  [code=3.30.1380.10, no name defined]                                                                                                                                                                                                     CATH domains
           Pfam domains (1) ------------Peptidase_M74-1tzpB01 B:35-272                                                                                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) ------------Peptidase_M74-1tzpB02 B:35-272                                                                                                                                                                                                                 Pfam domains (2)
         Sec.struct. author ............eeeee..eeeee..ee.......eee.hhhhh..eehhhhhhhhhhhhhhhhhh....eee......................eeeee........hhhhhhh...................hhhhhhhhhhhhh...eeeeeehhhhhhhhhhhh...hhhhh.eee......eeeeee.....................hhhhhhh..--------------...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tzp B  23 WQKITQPVPGSAQSIGSFSNGCIVGADTLPIQSEHYQVMRTDQRRYFGHPDLVMFIQRLSSQVSNLGMGTVLIGDMGMPAGGRFNGGHASHQTGLDVDIFLQLPKTRWTSAQLLRPQALDLVSRDGKHVVSTLWKPEIFSLIKLAAQDKDVTRIFVNPAIKQQLCLDAGTDRDWLRKVRPWFQHRAHMHVRLRCPADSLECEDQPLPPSGDGCGAELQSWFE--------------PPLPPSCQALLDEH 272
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242 |       -      |262       272
                                                                                                                                                                                                                                                       244            259
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_MD (20)

(-) Gene Ontology  (13, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MEPA_ECOLI | P0C0T5)
molecular function
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    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.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds 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.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in 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: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:0000270    peptidoglycan metabolic process    The chemical reactions and pathways involving peptidoglycans, any of a class of glycoconjugates found only in bacterial cell walls and consisting of strands of glycosaminoglycan cross-linked by oligopeptides to form a huge and rigid network.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain A,B   (MEPA_SHIFL | P0C0T6)
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: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.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds 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.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in 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:0000270    peptidoglycan metabolic process    The chemical reactions and pathways involving peptidoglycans, any of a class of glycoconjugates found only in bacterial cell walls and consisting of strands of glycosaminoglycan cross-linked by oligopeptides to form a huge and rigid network.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        MEPA_ECOLI | P0C0T5: 1u10
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(-) Related Entries Specified in the PDB File

1u10 MEPA, ACTIVE FORM WITH ZN