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(-) Description

Title :  THE X-RAY CRYSTAL STRUCTURE OF D-ALANYL-D-ALANINE LIGASE IN COMPLEX WITH ATP AND D-ALA-D-ALA
 
Authors :  S. Batson, V. Majce, A. J. Lloyd, D. Rea, C. W. G. Fishwick, K. J. Simmons, D. I. Roper
Date :  10 Sep 13  (Deposition) - 21 Jan 15  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Ddlb (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Batson, V. Majce, A. J. Lloyd, D. Rea, C. W. G. Fishwick, K. J. Simmons V. Fulop, D. I. Roper
D-Cycloserine Inhibition Occurs By A Novel Phosphoryl Intermediate: Prospects For Novel Antimicrobials Without Psychotic Side Effects.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - D-ALANINE--D-ALANINE LIGASE
    Chains: A, B
    EC Number: 6.3.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEX
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR-ROSETTA
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: D-ALA-D-ALA LIGASE, D-ALANYLALANINE SYNTHETASE, D-ALANYL-D-ALANINE LIGASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 17)

Asymmetric/Biological Unit (6, 17)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CO32Ligand/IonCARBONATE ION
3DAL4Ligand/IonD-ALANINE
4GOL2Ligand/IonGLYCEROL
5IMD1Ligand/IonIMIDAZOLE
6MG6Ligand/IonMAGNESIUM ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:97 , ILE A:142 , LYS A:144 , GLU A:148 , GLY A:149 , SER A:150 , SER A:151 , MET A:154 , GLU A:180 , LYS A:181 , TRP A:182 , LEU A:183 , GLU A:187 , PHE A:209 , TYR A:210 , LYS A:215 , ASP A:257 , MET A:259 , LEU A:269 , GLU A:270 , CO3 A:313 , MG A:1313 , MG A:1314 , HOH A:2254 , HOH A:2256 , HOH A:2326 , HOH A:2404BINDING SITE FOR RESIDUE ADP A 310
02AC2SOFTWAREGLY A:149 , SER A:150 , LYS A:215 , ARG A:255 , ASP A:257 , GLU A:270 , ASN A:272 , ADP A:310 , DAL A:311 , DAL A:312 , MG A:1313 , MG A:1314 , HOH A:2326BINDING SITE FOR RESIDUE CO3 A 313
03AC3SOFTWAREGLU A:270 , ASN A:272 , ADP A:310 , CO3 A:313 , MG A:1314 , HOH A:2254BINDING SITE FOR RESIDUE MG A1313
04AC4SOFTWAREASP A:257 , GLU A:270 , ADP A:310 , CO3 A:313 , MG A:1313 , HOH A:2326BINDING SITE FOR RESIDUE MG A1314
05AC5SOFTWAREGLU A:17 , VAL A:18 , TYR A:212 , LEU A:217 , ARG A:288 , HOH A:2051 , HOH A:2388BINDING SITE FOR RESIDUE GOL A1315
06AC6SOFTWAREPRO A:39 , ASP A:41 , GLN A:164 , ASP A:165 , ARG A:168 , HOH A:2081 , HOH A:2276 , HOH A:2405BINDING SITE FOR RESIDUE GOL A1316
07AC7SOFTWARELYS A:215 , TYR A:216 , HIS A:280 , HOH A:2281 , HOH A:2324 , HOH A:2374BINDING SITE FOR RESIDUE IMD A1317
08AC8SOFTWARELYS B:97 , ILE B:142 , LYS B:144 , GLU B:148 , GLY B:149 , SER B:150 , SER B:151 , MET B:154 , GLU B:180 , LYS B:181 , TRP B:182 , LEU B:183 , GLU B:187 , PHE B:209 , TYR B:210 , LYS B:215 , ASP B:257 , MET B:259 , GLU B:270 , CO3 B:313 , MG B:1307 , MG B:1308 , HOH B:2198 , HOH B:2200 , HOH B:2278 , HOH B:2356BINDING SITE FOR RESIDUE ADP B 310
09AC9SOFTWARESER B:150 , LYS B:215 , ARG B:255 , ASP B:257 , GLU B:270 , ASN B:272 , ADP B:310 , DAL B:311 , DAL B:312 , MG B:1307 , MG B:1308 , HOH B:2278BINDING SITE FOR RESIDUE CO3 B 313
10BC1SOFTWAREGLU B:270 , ASN B:272 , ADP B:310 , CO3 B:313 , MG B:1308 , HOH B:2198BINDING SITE FOR RESIDUE MG B1307
11BC2SOFTWAREASP B:257 , GLU B:270 , ADP B:310 , CO3 B:313 , MG B:1307 , HOH B:2278BINDING SITE FOR RESIDUE MG B1308
12BC3SOFTWAREHOH B:2224 , HOH B:2225 , HOH B:2358 , HOH B:2359 , HOH B:2360 , HOH B:2361BINDING SITE FOR RESIDUE MG B1310
13BC4SOFTWAREHIS B:280 , HOH B:2281 , HOH B:2285 , HOH B:2334 , HOH B:2336 , HOH B:2357BINDING SITE FOR RESIDUE MG B1309
14BC5SOFTWAREGLU A:15 , HIS A:63 , SER A:150 , TYR A:216 , ARG A:255 , GLY A:276 , SER A:281 , LEU A:282 , CO3 A:313 , HOH A:2149 , HOH A:2366BINDING SITE FOR DI-PEPTIDE DAL A 311 AND DAL A 312
15BC6SOFTWAREGLU B:15 , HIS B:63 , SER B:150 , TYR B:216 , ARG B:255 , GLY B:276 , SER B:281 , LEU B:282 , CO3 B:313 , HOH B:2108 , HOH B:2319BINDING SITE FOR DI-PEPTIDE DAL B 311 AND DAL B 312

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C5B)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Leu A:139 -Pro A:140
2Gly A:185 -Pro A:186
3Cys A:225 -Pro A:226
4Leu B:139 -Pro B:140
5Gly B:185 -Pro B:186
6Cys B:225 -Pro B:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C5B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C5B)

(-) Exons   (0, 0)

(no "Exon" information available for 4C5B)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhh......eeee.........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh......eeeeehhhhhh..hhhhhhhhhhhh..eeeee.........eee.hhhhhhhhhhhhhh...eeeeee.....eeeeeee..ee...eeee......hhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c5b A   1 MTDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQLKSMGFQKVFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKLLWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGSSVGMSKVVAENALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPSIRIQPSGTFYDYEAKYLSDETQYFCPAGLEASQEANLQALVLKAWTTLGCKGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVRILELAD 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300      


Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhh......eeee.........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh......eeeeehhhhhhh.hhhhhhhhhh....eeeee.........eee.hhhhhhhhhhhhh....eeeeee.....eeeeeee..ee...eeee......hhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c5b B   1 MTDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQLKSMGFQKVFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKLLWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGSSVGMSKVVAENALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPSIRIQPSGTFYDYEAKYLSDETQYFCPAGLEASQEANLQALVLKAWTTLGCKGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVRILELAD 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
   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  (0, 0)

(no "SCOP Domain" information available for 4C5B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C5B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C5B)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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        DDLB_ECOLI | P07862: 1iov 1iow 2dln 4c5a 4c5c

(-) Related Entries Specified in the PDB File

4c5a THE X-RAY CRYSTAL STRUCTURES OF D-ALANYL-D-ALANINE LIGASE IN COMPLEX ADP AND D-CYCLOSERINE PHOSPHATE
4c5c THE X-RAY CRYSTAL STRUCTURE OF D-ALANYL-D-ALANINE LIGASE IN COMPLEX WITH ADP AND D-ALA-D-ALA