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(-) Description

Title :  CRYSTAL STRUCTURE OF D-ALANINE:D-ALANINE LIGASE WITH ADP AND D-ALANINE FROM THERMUS THERMOPHIUS HB8
 
Authors :  Y. Kitamuta, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  22 Nov 07  (Deposition) - 27 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  D-Alanine-D-Alanine Ligase, Peptidoglycan Biosynthesis, Cell Shape, Cell Wall Biogenesis/Degradation, Peptidoglycan Synthesis, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kitamura, S. Yokoyama, S. Kuramitsu
Crystal Structure Of D-Alanine:D-Alanine Ligase With Adp And D-Alanine From Thermus Thermophius Hb8
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-ALANINE--D-ALANINE LIGASE
    ChainsA, B, C, D
    EC Number6.3.2.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-11A
    Expression System StrainBL21(DE3)
    Expression System Vector TypePLASMID
    Organism ScientificTHERMUS THERMOPHILUS
    StrainHB8

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2DAL2Ligand/IonD-ALANINE
3MG7Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2DAL1Ligand/IonD-ALANINE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2DAL1Ligand/IonD-ALANINE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:282 , ASN A:284BINDING SITE FOR RESIDUE MG A 811
02AC2SOFTWAREASP A:270 , GLU A:282BINDING SITE FOR RESIDUE MG A 812
03AC3SOFTWAREGLU B:282BINDING SITE FOR RESIDUE MG B 813
04AC4SOFTWAREGLU B:282BINDING SITE FOR RESIDUE MG B 814
05AC5SOFTWAREGLU C:282BINDING SITE FOR RESIDUE MG C 815
06AC6SOFTWAREGLU C:282BINDING SITE FOR RESIDUE MG C 816
07AC7SOFTWAREASP D:270 , GLU D:282BINDING SITE FOR RESIDUE MG D 817
08AC8SOFTWARELYS A:116 , PHE A:151 , LYS A:153 , GLY A:158 , SER A:159 , SER A:160 , ILE A:163 , GLU A:189 , LYS A:190 , ALA A:191 , LEU A:192 , GLU A:197 , TYR A:218 , PHE A:222 , TYR A:223 , LYS A:228 , PHE A:272 , ASN A:281 , GLU A:282BINDING SITE FOR RESIDUE ADP A 701
09AC9SOFTWARELYS B:116 , PHE B:151 , LYS B:153 , SER B:159 , SER B:160 , ILE B:163 , GLU B:189 , LYS B:190 , ALA B:191 , LEU B:192 , GLU B:197 , PHE B:272 , ASN B:281 , GLU B:282 , ALA C:220BINDING SITE FOR RESIDUE ADP B 702
10BC1SOFTWAREGLU A:13 , HIS A:82 , TYR A:229 , ARG A:268 , ASN A:284 , GLY A:288BINDING SITE FOR RESIDUE DAL A 801
11BC2SOFTWAREALA B:220 , LYS C:116 , PHE C:151 , LYS C:153 , GLY C:158 , SER C:159 , SER C:160 , ILE C:163 , GLU C:189 , LYS C:190 , ALA C:191 , LEU C:192 , GLU C:197 , PHE C:272 , ASN C:281 , GLU C:282BINDING SITE FOR RESIDUE ADP C 703
12BC3SOFTWARELYS D:116 , PHE D:151 , LYS D:153 , GLY D:158 , SER D:159 , SER D:160 , ILE D:163 , GLU D:189 , LYS D:190 , LEU D:192 , GLU D:197 , TYR D:218 , PHE D:222 , TYR D:223 , PHE D:272 , ASN D:281 , GLU D:282BINDING SITE FOR RESIDUE ADP D 704
13BC4SOFTWAREGLU D:13 , HIS D:82 , ARG D:268 , ASN D:284 , GLY D:288BINDING SITE FOR RESIDUE DAL D 802

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (16, 16)

Asymmetric Unit
No.Residues
1Phe A:65 -Pro A:66
2Pro A:148 -Pro A:149
3Ser A:193 -Pro A:194
4Ile A:238 -Pro A:239
5Phe B:65 -Pro B:66
6Pro B:148 -Pro B:149
7Ser B:193 -Pro B:194
8Ile B:238 -Pro B:239
9Phe C:65 -Pro C:66
10Pro C:148 -Pro C:149
11Ser C:193 -Pro C:194
12Ile C:238 -Pro C:239
13Phe D:65 -Pro D:66
14Pro D:148 -Pro D:149
15Ser D:193 -Pro D:194
16Ile D:238 -Pro D:239

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DALA_DALA_LIGASE_1PS00843 D-alanine--D-alanine ligase signature 1.DDL_THET882-93
 
 
 
  4A:82-93
B:82-93
C:82-93
D:82-93
2DALA_DALA_LIGASE_2PS00844 D-alanine--D-alanine ligase signature 2.DDL_THET8261-288
 
 
 
  4A:261-288
B:261-288
C:261-288
D:261-288
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DALA_DALA_LIGASE_1PS00843 D-alanine--D-alanine ligase signature 1.DDL_THET882-93
 
 
 
  2A:82-93
B:82-93
-
-
2DALA_DALA_LIGASE_2PS00844 D-alanine--D-alanine ligase signature 2.DDL_THET8261-288
 
 
 
  2A:261-288
B:261-288
-
-
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DALA_DALA_LIGASE_1PS00843 D-alanine--D-alanine ligase signature 1.DDL_THET882-93
 
 
 
  2-
-
C:82-93
D:82-93
2DALA_DALA_LIGASE_2PS00844 D-alanine--D-alanine ligase signature 2.DDL_THET8261-288
 
 
 
  2-
-
C:261-288
D:261-288

(-) Exons   (0, 0)

(no "Exon" information available for 2ZDH)

(-) 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:319
 aligned with DDL_THET8 | Q5SHZ3 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:319
                                    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       310         
            DDL_THET8     1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
               SCOP domains d2zdha1 A:1-114 automated matches                                                                                 d2zdha2 A:115-319 automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhh...eeeeee.....eehhhhhhhhhhhh.............hhhhh.eeee.........hhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhh......eeeee............eeeee.........eee.hhhhhhhhhhhhhh...eeeeee.....eeeeeeee.....eeeeeeeee......hhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zdh A   1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
                                    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       310         

Chain B from PDB  Type:PROTEIN  Length:312
 aligned with DDL_THET8 | Q5SHZ3 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:319
                                    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       310         
            DDL_THET8     1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
               SCOP domains d2zdhb1 B:1-114 automated matches                                                                                 d2zdhb2 B:115-319 automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhh...eeeeee.....eehhhhhhhhhhhh.............hhhhh.eeeee........hhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhh......eeeee............eeeee.........eee.hhhhhhhhhhhhh....eeeeee.....eeeeeeee.....eeeeeeeeee.....-------...eeee.....hhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zdh B   1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFY-------PGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  |      -|      240       250       260       270       280       290       300       310         
                                                                                                                                                                                                                                                        223     231                                                                                        

Chain C from PDB  Type:PROTEIN  Length:316
 aligned with DDL_THET8 | Q5SHZ3 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:319
                                    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       310         
            DDL_THET8     1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
               SCOP domains d2zdhc1 C:1-114 automated matches                                                                                 d2zdhc2 C:115-319 automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhh...eeeeee.....eehhhhhhhhhhh..............hhhhh.eeeee........hhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhh......eeeee............eeeee.........eee.hhhhhhhhhhhhh....eeeeee.....eeeeeeee.....eeeeeeeeee.....---.......eeee.....hhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zdh C   1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFY---TKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
                                    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       310         
                                                                                                                                                                                                                                                        223 227                                                                                            

Chain D from PDB  Type:PROTEIN  Length:319
 aligned with DDL_THET8 | Q5SHZ3 from UniProtKB/Swiss-Prot  Length:319

    Alignment length:319
                                    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       310         
            DDL_THET8     1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
               SCOP domains d2zdhd1 D:1-114 automated matches                                                                                 d2zdhd2 D:115-319 automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Dala_Dala_lig_N-2zdhD05 D:1-105                                                                          ----------------Dala_Dala_lig_C-2zdhD01 D:122-315                                                                                                                                                                 ---- Pfam domains (1)
           Pfam domains (2) Dala_Dala_lig_N-2zdhD06 D:1-105                                                                          ----------------Dala_Dala_lig_C-2zdhD02 D:122-315                                                                                                                                                                 ---- Pfam domains (2)
           Pfam domains (3) Dala_Dala_lig_N-2zdhD07 D:1-105                                                                          ----------------Dala_Dala_lig_C-2zdhD03 D:122-315                                                                                                                                                                 ---- Pfam domains (3)
           Pfam domains (4) Dala_Dala_lig_N-2zdhD08 D:1-105                                                                          ----------------Dala_Dala_lig_C-2zdhD04 D:122-315                                                                                                                                                                 ---- Pfam domains (4)
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhh...eeeeee.....eehhhhhhhhhhhh.............hhhhh.eeeee........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh......eeeee............eeeee.........eee.hhhhhhhhhhhhh....eeeeee.....eeeeeeee.....eeeeeeeee......hhhhhhh....eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2          ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zdh D   1 MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT 319
                                    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       310         

   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  (2, 8)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZDH)

(-) Pfam Domains  (2, 8)

Asymmetric Unit

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DDL_THET8 | Q5SHZ3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008716    D-alanine-D-alanine ligase activity    Catalysis of the reaction: 2 D-alanine + ATP = D-alanyl-D-alanine + ADP + 2 H(+) + phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DDL_THET8 | Q5SHZ32fb9 2yzg 2yzm 2yzn 2zdg 2zdq

(-) Related Entries Specified in the PDB File

2yzg FREE-FORM OF LIGASE
2yzm COCRYSTAL WITH LIGAND
2zdg COCRYSTAL WITH ADP RELATED ID: TTK003001114.5 RELATED DB: TARGETDB