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(-) Description

Title :  STRUCTURE OF MURE THE UDP-N-ACETYLMURAMYL TRIPEPTIDE SYNTHETASE FROM E. COLI
 
Authors :  E. J. Gordon, L. Chantala, O. Dideberg
Date :  19 Sep 00  (Deposition) - 13 Sep 01  (Release) - 21 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ligase, Peptidoglycan Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Gordon, B. Flouret, L. Chantalat, J. Van Heijenoort, D. Mengin-Lecreulx, O. Dideberg
Crystal Structure Of Udp-N-Acetylmuramoyl-L-Alanyl-D-Glutamate: Meso-Diaminopimelate Ligase From Escherichia Coli
J. Biol. Chem. V. 276 10999 2001
PubMed-ID: 11124264  |  Reference-DOI: 10.1074/JBC.M009835200

(-) Compounds

Molecule 1 - UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE--2,6- DIAMINOPIMELATE LIGASE
    Chains: A, B
    EC Number: 6.3.2.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MURE
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: UDP-N-ACETYLMURAMYL-TRIPEPTIDE BOUND IN ACTIVE SITE

 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  (5, 31)

Asymmetric Unit (5, 31)
No.NameCountTypeFull Name
1API2Ligand/Ion2,6-DIAMINOPIMELIC ACID
2CL1Ligand/IonCHLORIDE ION
3KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4MSE24Mod. Amino AcidSELENOMETHIONINE
5UAG2Ligand/IonURIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE
Biological Unit 1 (4, 15)
No.NameCountTypeFull Name
1API1Ligand/Ion2,6-DIAMINOPIMELIC ACID
2CL-1Ligand/IonCHLORIDE ION
3KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4MSE12Mod. Amino AcidSELENOMETHIONINE
5UAG1Ligand/IonURIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE
Biological Unit 2 (4, 15)
No.NameCountTypeFull Name
1API1Ligand/Ion2,6-DIAMINOPIMELIC ACID
2CL-1Ligand/IonCHLORIDE ION
3KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
4MSE12Mod. Amino AcidSELENOMETHIONINE
5UAG1Ligand/IonURIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:26 , ASP A:27 , SER A:28 , ARG A:29 , GLY A:42 , HIS A:43 , GLN A:44 , ALA A:45 , GLY A:47 , TYR A:50 , ASN A:156 , THR A:157 , THR A:158 , SER A:160 , SER A:184 , HIS A:186 , GLN A:190 , ARG A:192 , API A:1499 , HOH A:2085 , HOH A:2205 , HOH A:2206BINDING SITE FOR RESIDUE UAG A1498
2AC2SOFTWAREHIS A:210 , TYR A:357 , HIS A:359 , GLY A:386 , ARG A:389 , ASP A:413 , ASN A:414 , ARG A:416 , GLY A:464 , GLU A:468 , UAG A:1498BINDING SITE FOR RESIDUE API A1499
3AC3SOFTWARELEU B:26 , ASP B:27 , SER B:28 , ARG B:29 , PHE B:37 , GLY B:42 , HIS B:43 , GLN B:44 , ALA B:45 , GLY B:47 , TYR B:50 , ASN B:156 , THR B:157 , THR B:158 , SER B:160 , SER B:184 , HIS B:186 , GLN B:190 , ARG B:192 , HIS B:210 , API B:1499 , HOH B:2107 , HOH B:2184 , HOH B:2185 , HOH B:2186 , HOH B:2187BINDING SITE FOR RESIDUE UAG B1498
4AC4SOFTWARETYR B:357 , HIS B:359 , GLY B:386 , ARG B:389 , ASP B:413 , ASN B:414 , ARG B:416 , GLY B:464 , GLU B:468 , UAG B:1498BINDING SITE FOR RESIDUE API B1499

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E8C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1E8C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_MURE_ECOLI_001 *E344KMURE_ECOLI  ---  ---A/BE343K
2UniProtVAR_MURE_ECOLI_002 *A495SMURE_ECOLI  ---  ---A/BA494S
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_MURE_ECOLI_001 *E344KMURE_ECOLI  ---  ---AE343K
2UniProtVAR_MURE_ECOLI_002 *A495SMURE_ECOLI  ---  ---AA494S
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_MURE_ECOLI_001 *E344KMURE_ECOLI  ---  ---BE343K
2UniProtVAR_MURE_ECOLI_002 *A495SMURE_ECOLI  ---  ---BA494S
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1E8C)

(-) Exons   (0, 0)

(no "Exon" information available for 1E8C)

(-) 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:496
 aligned with MURE_ECOLI | P22188 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:496
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     495    
                                    13        23        33        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       493 |    
           MURE_ECOLI     4 RNLRDLLAPWVPDAPSRALREMTLDSRVAAAGDLFVAVVGHQADGRRYIPQAIAQGVAAIIAEAKDEATDGEIREMHGVPVIYLSQLNERLSALAGRFYHEPSDNLRLVGVTGTNGKTTTTQLLAQWSQLLGEISAVMGTVGNGLLGKVIPTENTTGSAVDVQHELAGLVDQGATFCAMEVSSHGLVQHRVAALKFAASVFTNLSRDHLDYHGDMEHYEAAKWLLYSEHHCGQAIINADDEVGRRWLAKLPDAVAVSMEDHINPNCHGRWLKATEVNYHDSGATIRFSSSWGDGEIESHLMGAFNVSNLLLALATLLALGYPLADLLKTAARLQPVCGRMEVFTAPGKPTVVVDYAHTPDALEKALQAARLHCAGKLWCVFGCGGDRDKGKRPLMGAIAEEFADVAVVTDDNPRTEEPRAIINDILAGMLDAGHAKVMEGRAEAVTCAVMQAKENDVVLVAGKGHEDYQIVGNQRLDYSDRVTVARLLGVIA----   -
               SCOP domains d1e8ca1 A:3-103 UDP-N-acetylmuramyl tripeptide synthetase MurE                                       d1e8ca3 A:104-337 UDP-N-acetylmuramyl tripeptide synthetase MurE                                                                                                                                                                          d1e8ca2 A:338-497 UDP-N-acetylmuramyl tripeptide synthetase MurE                                                                                                - SCOP domains
               CATH domains 1e8cA01 A:3-103  [code=3.40.1390.10, no name defined]                                                1e8cA02 A:104-341  [code=3.40.1190.10, no name defined]                                                                                                                                                                                       -1e8cA03 A:343-497  [code=3.90.190.20, no name defined]                                                                                                     - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh................hhhhh....eeee.......hhhhhhhhhhh...eeeee................eeeee.hhhhhhhhhhhhhh.hhhhh...eeee...hhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhhhh.........hhhhhhh.........eeee......hhhhhhhhhhhhhh.hhhhhh....eeeee..hhhhhhhhh.....eeee...........eeeeeeeeee....eeeeeee....eeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....eeeee......eeeee...hhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhh.eeee........hhhhhhhhhhh...hhhhh....hhhhhhhhhhhhh....eeeee......eeee..eeee.hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K------------------------------------------------------------------------------------------------------------------------------------------------------S---- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e8c A   3 RNLRDLLAPWVPDAPSRALREmTLDSRVAAAGDLFVAVVGHQADGRRYIPQAIAQGVAAIIAEAKDEATDGEIREmHGVPVIYLSQLNERLSALAGRFYHEPSDNLRLVGVTGTNGKTTTTQLLAQWSQLLGEISAVmGTVGNGLLGKVIPTENTTGSAVDVQHELAGLVDQGATFCAmEVSSHGLVQHRVAALKFAASVFTNLSRDHLDYHGDmEHYEAAkWLLYSEHHCGQAIINADDEVGRRWLAKLPDAVAVSmEDHINPNCHGRWLKATEVNYHDSGATIRFSSSWGDGEIESHLmGAFNVSNLLLALATLLALGYPLADLLKTAARLQPVCGRmEVFTAPGKPTVVVDYAHTPDALEKALQAARLHCAGKLWCVFGCGGDRDKGKRPLmGAIAEEFADVAVVTDDNPRTEEPRAIINDILAGmLDAGHAKVmEGRAEAVTCAVmQAKENDVVLVAGKGHEDYQIVGNQRLDYSDRVTVARLLGVIARSHH 498
                                    12        22 |      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       282       292       302|      312       322       332       342       352       362       372       382       392    |  402       412       422       432       442       452       462       472       482       492      
                                                24-MSE                                                78-MSE                                                       140-MSE                                  181-MSE                             217-MSE  |                                 260-MSE                                    303-MSE                                342-MSE                                                397-MSE                           431-MSE  440-MSE     452-MSE                                          
                                                                                                                                                                                                                                                       224-KCX                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:497
 aligned with MURE_ECOLI | P22188 from UniProtKB/Swiss-Prot  Length:495

    Alignment length:497
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      495    
                                    12        22        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       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492  |    
           MURE_ECOLI     3 DRNLRDLLAPWVPDAPSRALREMTLDSRVAAAGDLFVAVVGHQADGRRYIPQAIAQGVAAIIAEAKDEATDGEIREMHGVPVIYLSQLNERLSALAGRFYHEPSDNLRLVGVTGTNGKTTTTQLLAQWSQLLGEISAVMGTVGNGLLGKVIPTENTTGSAVDVQHELAGLVDQGATFCAMEVSSHGLVQHRVAALKFAASVFTNLSRDHLDYHGDMEHYEAAKWLLYSEHHCGQAIINADDEVGRRWLAKLPDAVAVSMEDHINPNCHGRWLKATEVNYHDSGATIRFSSSWGDGEIESHLMGAFNVSNLLLALATLLALGYPLADLLKTAARLQPVCGRMEVFTAPGKPTVVVDYAHTPDALEKALQAARLHCAGKLWCVFGCGGDRDKGKRPLMGAIAEEFADVAVVTDDNPRTEEPRAIINDILAGMLDAGHAKVMEGRAEAVTCAVMQAKENDVVLVAGKGHEDYQIVGNQRLDYSDRVTVARLLGVIA----   -
               SCOP domains d1e8cb1 B:2-103 UDP-N-acetylmuramyl tripeptide synthetase MurE                                        d1e8cb3 B:104-337 UDP-N-acetylmuramyl tripeptide synthetase MurE                                                                                                                                                                          d1e8cb2 B:338-498 UDP-N-acetylmuramyl tripeptide synthetase MurE                                                                                                  SCOP domains
               CATH domains -1e8cB01 B:3-103  [code=3.40.1390.10, no name defined]                                                1e8cB02 B:104-341  [code=3.40.1190.10, no name defined]                                                                                                                                                                                       -1e8cB03 B:343-484  [code=3.90.190.20, no name defined]                                                                                        -------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh................hhhhh....eeee.......hhhhhhhhhhh...eeeee........eee.....eeeee.hhhhhhhhhhhhhh.hhhhh...eeee...hhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhhhh.........hhhhhhh.........eeee......hhhhhhhhhhhhhh.hhhhhh....eeeee..hhhhhhhhh.....eeee...........eeeeeeeeee....eeeeeee....eeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....eeeee......eeeee...hhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhh.eeee........hhhhhhhhhhh............hhhhhhhhhhhhh....eeeee......eeee..eeee.hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K------------------------------------------------------------------------------------------------------------------------------------------------------S---- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e8c B   2 DRNLRDLLAPWVPDAPSRALREmTLDSRVAAAGDLFVAVVGHQADGRRYIPQAIAQGVAAIIAEAKDEATDGEIREmHGVPVIYLSQLNERLSALAGRFYHEPSDNLRLVGVTGTNGKTTTTQLLAQWSQLLGEISAVmGTVGNGLLGKVIPTENTTGSAVDVQHELAGLVDQGATFCAmEVSSHGLVQHRVAALKFAASVFTNLSRDHLDYHGDmEHYEAAkWLLYSEHHCGQAIINADDEVGRRWLAKLPDAVAVSmEDHINPNCHGRWLKATEVNYHDSGATIRFSSSWGDGEIESHLmGAFNVSNLLLALATLLALGYPLADLLKTAARLQPVCGRmEVFTAPGKPTVVVDYAHTPDALEKALQAARLHCAGKLWCVFGCGGDRDKGKRPLmGAIAEEFADVAVVTDDNPRTEEPRAIINDILAGmLDAGHAKVmEGRAEAVTCAVmQAKENDVVLVAGKGHEDYQIVGNQRLDYSDRVTVARLLGVIARSHH 498
                                    11        21  |     31        41        51        61        71      | 81        91       101       111       121       131       141       151       161       171       181       191       201       211     | 221  |    231       241       251       261       271       281       291       301 |     311       321       331       341|      351       361       371       381       391     | 401       411       421       431       441       451|      461       471       481       491       
                                                 24-MSE                                                78-MSE                                                       140-MSE                                  181-MSE                             217-MSE  |                                 260-MSE                                    303-MSE                                342-MSE                                                397-MSE                           431-MSE  440-MSE     452-MSE                                          
                                                                                                                                                                                                                                                        224-KCX
   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  (3, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E8C)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MURE_ECOLI | P22188)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008765    UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity    Catalysis of the reaction: meso-2,6-diaminopimelate + ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate = ADP + 2 H(+) + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminoheptanedioate.
    GO:0016881    acid-amino acid ligase activity    Catalysis of the ligation of an acid to an amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    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:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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