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(-) Description

Title :  CRYSTAL STRUCTURE OF VANX
 
Authors :  S. D. Pratt, L. Katz, J. M. Severin, T. Holzman, C. H. Park
Date :  03 Oct 03  (Deposition) - 15 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Vanx, E. Faecium, Dipeptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. E. Bussiere, S. D. Pratt, L. Katz, J. M. Severin, T. Holzman, C. H. Park
The Structure Of Vanx Reveals A Novel Amino-Dipeptidase Involved In Mediating Transposon-Based Vancomycin Resistance
Mol. Cell V. 2 75 1998
PubMed-ID: 9702193  |  Reference-DOI: 10.1016/S1097-2765(00)80115-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-ALANYL-D-ALANINE DIPEPTIDASE
    Chains: A, B, C, D, E, F
    EC Number: 3.4.13.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI STR. K12 SUBSTR. W3110
    Expression System Plasmid: PGW1
    Expression System Strain: W3110
    Expression System Taxid: 316407
    Expression System Vector Type: PLASMID
    Gene: VANX
    Organism Scientific: ENTEROCOCCUS FAECIUM
    Organism Taxid: 1352
    Synonym: D-ALA-D-ALA DIPEPTIDASE, VANCOMYCIN B-TYPE RESISTANCE PROTEIN VANX

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1ZN6Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:116 , ASP A:123 , HIS A:184 , HOH A:205BINDING SITE FOR RESIDUE ZN A 203
2AC2SOFTWAREHIS B:116 , ASP B:123 , HIS B:184 , HOH B:204BINDING SITE FOR RESIDUE ZN B 203
3AC3SOFTWAREHIS C:116 , ASP C:123 , HIS C:184BINDING SITE FOR RESIDUE ZN C 203
4AC4SOFTWAREHIS D:116 , ASP D:123 , HIS D:184 , HOH D:204BINDING SITE FOR RESIDUE ZN D 203
5AC5SOFTWAREHIS E:116 , ASP E:123 , HIS E:184 , HOH E:205BINDING SITE FOR RESIDUE ZN E 203
6AC6SOFTWAREHIS F:116 , ASP F:123 , HIS F:184 , HOH F:205BINDING SITE FOR RESIDUE ZN F 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R44)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R44)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R44)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R44)

(-) Exons   (0, 0)

(no "Exon" information available for 1R44)

(-) 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:202
 aligned with VANX_ENTFC | Q06241 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
           VANX_ENTFC     1 MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK 202
               SCOP domains d1r44a_ A: D-Ala-D-Ala dipeptidase VanX                                                                                                                                                                    SCOP domains
               CATH domains 1r44A00 A:1-202  [code=3.30.1380.10, no name defined]                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhh....ee.hhhhh.................eeehhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhh......hhhhhh.....hhhhhh......hhhhhh.eeeeeeee................hhhhh......hhhhhhhhhhhhhhhhh..eee......eeee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r44 A   1 MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  


Chain B from PDB  Type:PROTEIN  Length:202
 aligned with VANX_ENTFC | Q06241 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
           VANX_ENTFC     1 MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK 202
               SCOP domains d1r44b_ B: D-Ala-D-Ala dipeptidase VanX                                                                                                                                                                    SCOP domains
               CATH domains 1r44B00 B:1-202  [code=3.30.1380.10, no name defined]                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhh....ee.hhhhh.................eeehhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhh......hhhhhh...hhhhh.........hhhhhh.eeeeeeee................hhhhh......hhhhhhhhhhhhhhhhh..eee......eeee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r44 B   1 MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  


Chain C from PDB  Type:PROTEIN  Length:202
 aligned with VANX_ENTFC | Q06241 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
           VANX_ENTFC     1 MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK 202
               SCOP domains d1r44c_ C: D-Ala-D-Ala dipeptidase VanX                                                                                                                                                                    SCOP domains
               CATH domains 1r44C00 C:1-202  [code=3.30.1380.10, no name defined]                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhh....ee.hhhhh.................eeehhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhh......hhhhhh....hhhhh........hhhhhh.eeeeeeee................hhhhh......hhhhhhhhhhhhhhhhh..eee......eeee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r44 C   1 MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  


Chain D from PDB  Type:PROTEIN  Length:202
 aligned with VANX_ENTFC | Q06241 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
           VANX_ENTFC     1 MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK 202
               SCOP domains d1r44d_ D: D-Ala-D-Ala dipeptidase VanX                                                                                                                                                                    SCOP domains
               CATH domains 1r44D00 D:1-202  [code=3.30.1380.10, no name defined]                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhh....ee.hhhhh.................eeehhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhh......hhhhhh...hhhhhhhh......hhhhhh.eeeeeeee................hhhhh......hhhhhhhhhhhhhhhhh..ee.......eeee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r44 D   1 MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  


Chain E from PDB  Type:PROTEIN  Length:202
 aligned with VANX_ENTFC | Q06241 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
           VANX_ENTFC     1 MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK 202
               SCOP domains d1r44e_ E: D-Ala-D-Ala dipeptidase VanX                                                                                                                                                                    SCOP domains
               CATH domains 1r44E00 E:1-202  [code=3.30.1380.10, no name defined]                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhh....ee.hhhhh.................eeehhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhh......hhhhhh.................hhhhhh.eeeeeeee................hhhhh......hhhhhhhhhhhhhhhhh..eee......eeee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r44 E   1 MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  


Chain F from PDB  Type:PROTEIN  Length:202
 aligned with VANX_ENTFC | Q06241 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
           VANX_ENTFC     1 MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK 202
               SCOP domains d1r44f_ F: D-Ala-D-Ala dipeptidase VanX                                                                                                                                                                    SCOP domains
               CATH domains 1r44F00 F:1-202  [code=3.30.1380.10, no name defined]                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhh....ee.hhhhh.................eeehhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhh......hhhhhh...hhhhhhhh......hhhhhh.eeeeeeee................hhhhh......hhhhhhhhhhhhhhhhh..ee.......eeee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r44 F   1 MEIGFTFLDEIVHGVRWDAKYATWDNFTGKPVDGYEVNRIVGTYELAESLLKAKELAATQGYGLLLWDGYRPKRAVNCFMQWAAQPENNLTKESYYPNIDRTEMISKGYVASKSSHSRGSAIDLTLYRLDTGELVPMGSRFDFMDERSHHAANGISCNEAQNRRRLRSIMENSGFEAYSLEWWHYVLRDEPYPNSYFDFPVK 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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  (1, 6)

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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1R44)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (VANX_ENTFC | Q06241)
molecular function
    GO:0016805    dipeptidase activity    Catalysis of the hydrolysis of a dipeptide.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.

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  1r44
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  VANX_ENTFC | Q06241
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  3.4.13.-
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 Related Entries

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

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(no "Related Entries Specified in the PDB File" available for 1R44)