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(-) Description

Title :  D-ALANYL-D-LACATE LIGASE
 
Authors :  D. I. Roper
Date :  03 Jul 00  (Deposition) - 28 Jun 01  (Release) - 21 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Ligase, Cell Wall, Antibiotic Resistance, Membrane, Peptidoglycan Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. I. Roper, T. Huyton, A. Vagin, G. Dodson
The Molecular Basis Of Vancomycin Resistance In Clinically Releveant Enterococci: Crsytal Structure Of D-Alanyl-D-Lactate Ligase (Vana)
Proc. Natl. Acad. Sci. Usa V. 97 8921 2000
PubMed-ID: 10908650  |  Reference-DOI: 10.1073/PNAS.150116497

(-) Compounds

Molecule 1 - VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA
    Cellular Location: CYTOPLASM
    Chains: A
    EC Number: 6.1.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: VANA
    Organism Scientific: ENTEROCOCCUS FAECIUM
    Organism Taxid: 1352
    Strain: BM41417
    Synonym: D-ALANINE--D-LACTATE LIGASE, VANA LIGASE
 
Molecule 2 - VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA
    Cellular Location: CYTOPLASM
    Chains: B
    EC Number: 6.1.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: VANA
    Organism Scientific: ENTEROCOCCUS FAECIUM
    Organism Taxid: 1352
    Strain: BM41417
    Synonym: D-ALANINE--D-LACTATE LIGASE, VANA LIGASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 25)

Asymmetric Unit (5, 25)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL14Ligand/IonGLYCEROL
3MG4Ligand/IonMAGNESIUM ION
4PHY2Ligand/Ion1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID
5SO43Ligand/IonSULFATE ION
Biological Unit 1 (4, 42)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL28Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4PHY4Ligand/Ion1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID
5SO46Ligand/IonSULFATE ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:133 , PHE A:169 , LYS A:171 , SER A:175 , GLY A:176 , SER A:177 , SER A:178 , GLU A:207 , GLN A:208 , VAL A:210 , GLU A:214 , LEU A:236 , ILE A:240 , PHE A:241 , PHE A:294 , ASN A:304 , GLU A:305 , PHY A:355 , MG A:360 , MG A:365 , HOH A:2095 , HOH A:2112 , HOH A:2151 , HOH A:2166 , HOH A:2167BINDING SITE FOR RESIDUE ADP A 350
02AC2SOFTWAREGLU A:16 , SER A:177 , PHE A:241 , ILE A:243 , HIS A:244 , ARG A:290 , GLU A:305 , ASN A:307 , GLY A:311 , SER A:316 , ARG A:317 , ADP A:350 , MG A:360 , MG A:365 , HOH A:2097 , HOH A:2154 , HOH A:2167 , HOH A:2168 , HOH A:2169BINDING SITE FOR RESIDUE PHY A 355
03AC3SOFTWAREGLU A:305 , ASN A:307 , ADP A:350 , PHY A:355 , HOH A:2095BINDING SITE FOR RESIDUE MG A 360
04AC4SOFTWAREGLU A:305 , ADP A:350 , PHY A:355 , HOH A:2151 , HOH A:2167BINDING SITE FOR RESIDUE MG A 365
05AC5SOFTWARELYS B:133 , PHE B:169 , LYS B:171 , GLY B:176 , SER B:177 , SER B:178 , GLU B:207 , GLN B:208 , ALA B:209 , VAL B:210 , GLU B:214 , LEU B:236 , ILE B:240 , PHE B:241 , PHE B:294 , ASN B:304 , GLU B:305 , PHY B:355 , MG B:360 , MG B:365 , HOH B:2150 , HOH B:2171 , HOH B:2172BINDING SITE FOR RESIDUE ADP B 350
06AC6SOFTWAREGLU B:16 , SER B:177 , HIS B:244 , ARG B:290 , GLU B:305 , ASN B:307 , GLY B:311 , SER B:316 , ARG B:317 , ADP B:350 , MG B:360 , MG B:365 , HOH B:2054 , HOH B:2096 , HOH B:2160 , HOH B:2171 , HOH B:2173BINDING SITE FOR RESIDUE PHY B 355
07AC7SOFTWAREGLY B:176 , GLU B:305 , ASN B:307 , ADP B:350 , PHY B:355 , HOH B:2094BINDING SITE FOR RESIDUE MG B 360
08AC8SOFTWAREGLU B:305 , ADP B:350 , PHY B:355 , HOH B:2150 , HOH B:2171BINDING SITE FOR RESIDUE MG B 365
09AC9SOFTWAREHOH A:2143 , ARG B:174 , LYS B:203 , HOH B:2103 , HOH B:3002BINDING SITE FOR RESIDUE SO4 B1342
10BC1SOFTWAREARG A:174 , LYS A:203 , HOH A:2109 , HOH A:3003 , HOH A:3004 , HOH B:2068BINDING SITE FOR RESIDUE SO4 A1343
11BC2SOFTWAREASP A:105 , ARG A:174 , HOH A:3007 , HOH A:3008 , GLN B:125 , HOH B:3009 , HOH B:3010BINDING SITE FOR RESIDUE SO4 A1344
12BC3SOFTWARESER A:66 , LYS A:81 , ARG A:242 , GLN A:245 , GLU A:246 , VAL A:247BINDING SITE FOR RESIDUE GOL A1345
13BC4SOFTWARESER B:265 , ALA B:266BINDING SITE FOR RESIDUE GOL B1343
14BC5SOFTWAREARG B:3 , LYS B:33 , GLU B:34BINDING SITE FOR RESIDUE GOL B1344
15BC6SOFTWARELEU B:339 , ALA B:340 , LEU B:341BINDING SITE FOR RESIDUE GOL B1345
16BC7SOFTWAREGLU A:62 , LYS A:183 , TYR A:238 , GLY A:239BINDING SITE FOR RESIDUE GOL A1346
17BC8SOFTWAREHIS A:84 , SER A:178 , ARG A:242 , GLN A:245BINDING SITE FOR RESIDUE GOL A1347
18BC9SOFTWAREASN A:2 , ARG A:3BINDING SITE FOR RESIDUE GOL A1348
19CC1SOFTWARELYS A:155 , GLU A:195 , HOH A:2106BINDING SITE FOR RESIDUE GOL A1349
20CC2SOFTWAREGLU B:37 , LEU B:39 , MET B:51 , ASN B:89BINDING SITE FOR RESIDUE GOL B1346
21CC3SOFTWAREGLU B:26 , PHE B:312 , THR B:313 , SER B:314 , LEU B:329 , HOH B:3011BINDING SITE FOR RESIDUE GOL B1347
22CC4SOFTWAREGLU A:62 , ASN A:63 , CYS A:64 , TYR A:65 , SER A:66BINDING SITE FOR RESIDUE GOL A 990
23CC5SOFTWARELYS A:155BINDING SITE FOR RESIDUE GOL A 996
24CC6SOFTWARELYS A:5 , GLU A:37 , ASN A:89BINDING SITE FOR RESIDUE GOL A1350
25CC7SOFTWARELYS B:50 , TYR B:65 , HOH B:3012 , HOH B:3013BINDING SITE FOR RESIDUE GOL B1348

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:52 -A:64
2B:52 -B:64

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:166 -Pro A:167
2Val A:260 -Pro A:261
3Tyr B:166 -Pro B:167
4Val B:260 -Pro B:261

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E4E)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DALA_DALA_LIGASE_1PS00843 D-alanine--D-alanine ligase signature 1.VANA_ENTFC99-110
 		  2A:99-110
B:99-110
2DALA_DALA_LIGASE_2PS00844 D-alanine--D-alanine ligase signature 2.VANA_ENTFC283-311
 		  2A:283-311
B:283-311
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DALA_DALA_LIGASE_1PS00843 D-alanine--D-alanine ligase signature 1.VANA_ENTFC99-110
 		  4A:99-110
B:99-110
2DALA_DALA_LIGASE_2PS00844 D-alanine--D-alanine ligase signature 2.VANA_ENTFC283-311
 		  4A:283-311
B:283-311

(-) Exons   (0, 0)

(no "Exon" information available for 1E4E)

(-) 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:341
 aligned with VANA_ENTFC | P25051 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:341
                                    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 
           VANA_ENTFC     2 NRIKVAILFGGCSEEHDVSVKSAIEIAANINKEKYEPLYIGITKSGVWKMCEKPCAEWENDNCYSAVLSPDKKMHGLLVKKNHEYEINHVDVAFSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDKSLTYIVAKNAGIATPAFWVINKDDRPVAATFTYPVFVKPARSGSSFGVKKVNSADELDYAIESARQYDSKILIEQAVSGCEVGCAVLGNSAALVVGEVDQIRLQYGIFRIHQEVEPEKGSENAVITVPADLSAEERGRIQETAKKIYKALGCRGLARVDMFLQDNGRIVLNEVNTLPGFTSYSRYPRMMAAAGIALPELIDRLIVLALK 342
               SCOP domains d1e4ea1 A:2-131 D-alanine:D-lactate ligase VanA, N-domain                                                                         d1e4ea2 A:132-342 D-alanine:D-lactate ligase VanA, C-domain                                                                                                                                                         SCOP domains
               CATH domains 1e4eA03 A:2-121  [code=3.40.50.20, no name defined]                                                                     1e4eA01                  --1e4eA02 A:149-206 ATP-grasp fold, A domain                ----1e4eA01 A:122-146,A:211-342 ATP-grasp fold, B domain                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee.....eeee..............eee.......eeeeee..eeeeee..eeee.........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh......eeee......hhhhh...eeeee.........eee.hhhhhhhhhhhhh.....eeeee....eeeeeeeeee.........eeeee.....hhhhh.hhhhh...eee......hhhhhhhhhhhhhhhhhhh..eeeeeeeeee.....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------DALA_DALA_LI----------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           ------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e4e A   2 NRIKVAILFGGCSEEHDVSVKSAIEIAANINKEKYEPLYIGITKSGVWKMCEKPCAEWENENCYSAVLSPDKKMHGLLVKKNHEYEINHVDVAFSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDKSLTYIVAKNAGIATPAFWVINKDDRPVAATFTYPVFVKPARSGSSFGVKKVNSADELDYAIESARQYDSKILIEQAVSGCEVGCAVLGNSAALVVGEVDQIRLQYGIFRIHQEVEPEKGSENAVITVPADLSAEERGRIQETVKKIYKTLGCRGLARVDMFLQDNGRIVLNEVNTLPGFTSYSRYPRMMAAAGISLPELIDRLIVLALK 342
                                    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 


Chain B from PDB  Type:PROTEIN  Length:340
 aligned with VANA_ENTFC | P25051 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:340
                                    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
           VANA_ENTFC     2 NRIKVAILFGGCSEEHDVSVKSAIEIAANINKEKYEPLYIGITKSGVWKMCEKPCAEWENDNCYSAVLSPDKKMHGLLVKKNHEYEINHVDVAFSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDKSLTYIVAKNAGIATPAFWVINKDDRPVAATFTYPVFVKPARSGSSFGVKKVNSADELDYAIESARQYDSKILIEQAVSGCEVGCAVLGNSAALVVGEVDQIRLQYGIFRIHQEVEPEKGSENAVITVPADLSAEERGRIQETAKKIYKALGCRGLARVDMFLQDNGRIVLNEVNTLPGFTSYSRYPRMMAAAGIALPELIDRLIVLAL 341
               SCOP domains d1e4eb1 B:2-131 D-alanine:D-lactate ligase VanA, N-domain                                                                         d1e4eb2 B:132-341 D-alanine:D-lactate ligase VanA, C-domain                                                                                                                                                        SCOP domains
               CATH domains 1e4eB03 B:2-121  [code=3.40.50.20, no name defined]                                                                     1e4eB01                  --1e4eB02 B:149-206 ATP-grasp fold, A domain                ----1e4eB01 B:122-146,B:211-341 ATP-grasp fold, B domain                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhh......eeeeeeee.....eeee..............eee.......eeeee....eeeee..eeee.........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh......eeee......hhhhh...eeeee.........eee.hhhhhhhhhhhhh.....eeeee....eeeeeeeee..........eeeee.....hhhhh.hhhhh...eeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------DALA_DALA_LI----------------------------------------------------------------------------------------------------------------------------------------------------------------------------DALA_DALA_LIGASE_2           ------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e4e B   2 NRIKVAILFGGCSEEHDVSVKSAIEIAANINKEKYEPLYIGITKSGVWKMCEKPCAEWENENCYSAVLSPDKKMHGLLVKKNHEYEINHVDVAFSALHGKSGEDGSIQGLFELSGIPFVGCDIQSSAICMDKSLTYIVAKNAGIATPAFWVINKDDRPVAATFTYPVFVKPARSGSSFGVKKVNSADELDYAIESARQYDSKILIEQAVSGCEVGCAVLGNSAALVVGEVDQIRLQYGIFRIHQEVEPEKGSENAVITVPADLSAEERGRIQETVKKIYKTLGCRGLARVDMFLQDRGRIVLNEVNTLPGFTSYSRYPRMMAAAGISLPELIDRLIVLAL 341
                                    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
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
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 1E4E)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (VANA_ENTFC | P25051)
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.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  1e4e
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    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  VANA_ENTFC | P25051
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1E4E)

(-) Related Entries Specified in the PDB File

1iov COMPLEX OF D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHONATE
1iow COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE