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(-) Description

Title :  D-ALANINE--D-ALANINE LIGASE FROM YERSINIA PESTIS
 
Authors :  J. Osipiuk, B. Nocek, R. Mulligan, L. Papazisi, W. F. Anderson, A. Joach Center For Structural Genomics Of Infectious Diseases (Csgi
Date :  15 Dec 11  (Deposition) - 28 Dec 11  (Release) - 28 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Peptidoglycan Synthesis, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, B. Nocek, R. Mulligan, L. Papazisi, W. F. Anderson, A. Joachimiak
D-Alanine--D-Alanine Ligase From Yersinia Pestis.
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: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DDL, DDLB, Y3624, YPO0557, YP_3627
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 214092
    Strain: CO92
    Synonym: D-ALA-D-ALA LIGASE, D-ALANYLALANINE SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
2PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:25 , ALA A:28 , PHE A:294 , ALA B:25BINDING SITE FOR RESIDUE PGE B 501
2AC2SOFTWAREPRO A:113 , LYS A:181 , ASP A:261 , TYR A:267BINDING SITE FOR RESIDUE PEG A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V4Z)

(-) 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 3V4Z)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DALA_DALA_LIGASE_1PS00843 D-alanine--D-alanine ligase signature 1.DDL_YERPE63-74
 		  2A:63-74
B:63-74
2DALA_DALA_LIGASE_2PS00844 D-alanine--D-alanine ligase signature 2.DDL_YERPE248-276
 		  2A:248-276
B:248-276

(-) Exons   (0, 0)

(no "Exon" information available for 3V4Z)

(-) 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:293
 aligned with DDL_YERPE | Q8ZIE7 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:305
                                    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     
            DDL_YERPE     2 AEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLKEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTKLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHEGSSVGMSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSIRIQPPGVFYDYDAKYLSDKTQYFCPSGLSDESEQQLAALALQAYHALDCSGWGRVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILMLAD 306
               SCOP domains d3v4za1 A:2-96 automated matches                                                               d3v4za2 A:97-306 automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhhhhhhh..eeeee....hhhhh......eeee.........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh......eeeeehhhhh..hhhhhhhhhhhhh..eeeee.........eee.hhhhhhhhhhhhhh...eeeeee.....eeeeeee..ee...eeee...------------..eee.....hhhhhhhhhhhhhhhhhh.....eeeeeeee.....eeeeeee........hhhhhhhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           ------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v4z A   2 AEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLKEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTKLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHEGSSVGMSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSIRIQPPG------------KTQYFCPSGLSDESEQQLAALALQAYHALDCSGWGRVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILMLAD 306
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     |   -       221       231       241       251       261       271       281       291       301     
                                                                                                                                                                                                                                       207          220                                                                                      


Chain B from PDB  Type:PROTEIN  Length:287
 aligned with DDL_YERPE | Q8ZIE7 from UniProtKB/Swiss-Prot  Length:306

    Alignment length: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      
            DDL_YERPE     1 MAEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLKEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTKLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHEGSSVGMSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSIRIQPPGVFYDYDAKYLSDKTQYFCPSGLSDESEQQLAALALQAYHALDCSGWGRVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILMLAD 306
               SCOP domains d3v4zb1 B:1-96 automated matches                                                                d3v4zb2 B:97-306 automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhhhhhhhhh...eeeee....hhhhh......eeee.........hhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhh..eeeee..-----..eee....hhhhhhhhhh....eeeeee.....eeeeeee..eeeeeeeee..--------------.eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee........hhhhhhhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------DALA_DALA_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           ------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3v4z B   1 MAEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLKEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTKLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSH-----GMSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSIRIQPP--------------TQYFCPSGLSDESEQQLAALALQAYHALDCSGWGRVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILMLAD 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      |  -  |    160       170       180       190       200     |   -         -|      230       240       250       260       270       280       290       300      
                                                                                                                                                                            147   153                                                  206            221
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V4Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V4Z)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DDL_YERPE | Q8ZIE7)
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_YERPE | Q8ZIE7: 4zqi 5bpf 5bph 5c1o 5c1p

(-) Related Entries Specified in the PDB File

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