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(-) Description

Title :  UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
 
Authors :  J. Bertrand, G. Auger, L. Martin, E. Fanchon, D. Blanot, D. Le Beller, J. Van Heijenoort, O. Dideberg
Date :  09 Mar 99  (Deposition) - 15 Mar 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym./Biol. Unit :  A
Keywords :  Ligase, Peptidoglycan Synthesis, Murd, Adp-Forming Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Bertrand, G. Auger, L. Martin, E. Fanchon, D. Blanot, D. Le Beller, J. Van Heijenoort, O. Dideberg
Determination Of The Murd Mechanism Through Crystallographic Analysis Of Enzyme Complexes.
J. Mol. Biol. V. 289 579 1999
PubMed-ID: 10356330  |  Reference-DOI: 10.1006/JMBI.1999.2800
(for further references see the PDB file header)

(-) Compounds

Molecule 1
    Chains: A
    EC Number: 6.3.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: JM83 (PMLD58)
    Expression System Taxid: 562
    Gene: MURD GENE
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: JM83 (PMLD58)
    Synonym: MURD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
2SO41Ligand/IonSULFATE ION
3UAG1Ligand/IonURIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE
4UNX8Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:113 , GLY A:114 , LYS A:115 , SER A:116 , THR A:117 , ARG A:302 , LYS A:319 , HOH A:643 , HOH A:646BINDING SITE FOR RESIDUE SO4 A 461
02AC2SOFTWAREGLY A:14 , LEU A:15 , THR A:16 , ASP A:35 , THR A:36 , ARG A:37 , SER A:71 , PRO A:72 , GLY A:73 , GLY A:137 , ASN A:138 , GLY A:140 , SER A:159 , PHE A:161 , GLN A:162 , HIS A:183 , THR A:321 , LYS A:348 , ALA A:414 , SER A:415 , ASN A:421 , PHE A:422 , HOH A:501 , HOH A:502 , HOH A:529 , HOH A:554 , HOH A:565 , HOH A:594 , HOH A:600 , HOH A:684 , HOH A:906 , HOH A:912 , HOH A:956 , HOH A:958 , UNX A:986 , UNX A:990 , UNX A:991 , UNX A:992 , UNX A:993BINDING SITE FOR RESIDUE UAG A 460
03AC3SOFTWAREASN A:138 , ILE A:139 , UAG A:460 , HOH A:624 , HOH A:904 , UNX A:987 , UNX A:990BINDING SITE FOR RESIDUE UNX A 986
04AC4SOFTWARESER A:116 , ASN A:138 , GLU A:157 , LYS A:319 , UNX A:986 , UNX A:988 , UNX A:989 , UNX A:990BINDING SITE FOR RESIDUE UNX A 987
05AC5SOFTWARELYS A:319 , HOH A:942 , UNX A:987 , UNX A:989 , UNX A:990 , UNX A:991 , UNX A:992 , UNX A:993BINDING SITE FOR RESIDUE UNX A 988
06AC6SOFTWAREASN A:138 , UNX A:987 , UNX A:988 , UNX A:990 , UNX A:991 , UNX A:992 , UNX A:993BINDING SITE FOR RESIDUE UNX A 989
07AC7SOFTWAREASN A:138 , UAG A:460 , UNX A:986 , UNX A:987 , UNX A:988 , UNX A:989 , UNX A:991 , UNX A:992BINDING SITE FOR RESIDUE UNX A 990
08AC8SOFTWAREPHE A:422 , UAG A:460 , UNX A:988 , UNX A:989 , UNX A:990 , UNX A:992 , UNX A:993BINDING SITE FOR RESIDUE UNX A 991
09AC9SOFTWAREASN A:138 , UAG A:460 , HOH A:920 , UNX A:988 , UNX A:989 , UNX A:990 , UNX A:991 , UNX A:993BINDING SITE FOR RESIDUE UNX A 992
10BC1SOFTWARETHR A:321 , UAG A:460 , HOH A:920 , HOH A:942 , UNX A:988 , UNX A:989 , UNX A:991 , UNX A:992BINDING SITE FOR RESIDUE UNX A 993

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:208 -A:227

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UAG)

(-) Exons   (0, 0)

(no "Exon" information available for 4UAG)

(-) 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:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4uaga1 A:1-93 UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD                        d4uaga3 A:94-297 UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD                                                                                                                             d4uaga2 A:298-437 UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD                                                                     SCOP domains
               CATH domains 4uagA01 A:1-92 NAD(P)-binding Rossmann-like Domain                                          4uagA02 A:93-298  [code=3.40.1190.10, no name defined]                                                                                                                                                4uagA03 A:299-434  [code=3.90.190.20, no name defined]                                                                                  --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee..hhhhhhhhhhhhh.....eeee....hhhhhhh.....eee...hhhhhhhh.eeee.......hhhhhhhhhh..eeehhhhhhhh.....eeeee...hhhhhhhhhhhhhhhh...eeeee....hhhhhh.....eeeee.hhhhhhh.......eeee......hhhhh.hhhhhhhhh.hhhhh...eeeee..hhhhh....eee......eeee...eeee..eeeee.hhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.......eeeeee..eeeee.....hhhhhhhhhh.......eeeeee.......hhhhhhhh....eeeeee..hhhhhhhhhhh.eee..hhhhhhhhhhhhh....eeee...........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uag A   1 ADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAVERHTGSLNDEWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCREAQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDECELYVLELSSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAkLRIYENAKVCVVNADDALTMPIRCVSFGVNMGDYHLNHETWLRVKGEKVLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFEVVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSPLARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPRVQPGDMVLLSPACASLDQFKNFEQRGNEFARLAKELG 437
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220|      235     ||248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428         
                                                                                                                                                                                                                               198-KCX               220|            241|                                                                                                                                                                                                
                                                                                                                                                                                                                                                      226             245
   Legend:   → Mismatch (orange background)
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  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, 3)

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

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  6.3.2.9
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 Related Entries

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

UniProtKB/Swiss-Prot
        MURD_ECOLI | P14900: 1e0d 1eeh 1uag 2jff 2jfg 2jfh 2uag 2uuo 2uup 2vtd 2vte 2wjp 2x5o 2xpc 2y1o 2y66 2y67 2y68 3uag 5a5e 5a5f

(-) Related Entries Specified in the PDB File

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