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(-) Description

Title :  CRYSTAL STRUCTURE OF ENTEROCOCCUS FAECALIS NICOTINATE PHOSPHORIBOSYLTRANSFERASE WITH MALONATE AND PHOSPHATE BOUND
 
Authors :  Y. Patskovsky, R. Toro, S. R. Wasserman, S. C. Almo, S. K. Burley, New Yo Research Center For Structural Genomics (Nysgxrc), New York Structural Genomics Research Consortium (Nysgrc)
Date :  30 Sep 13  (Deposition) - 23 Oct 13  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Structural Genomics, Psi, Rotein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, New York Structural Genomics Research Consortium, Nysgrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Toro, S. R. Wasserman, S. K. Burley, S. C. Almo
Crystal Structure Of Enterococcus Faecalis Nicotinate Phosphoribosyltransferase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NICOTINATE PHOSPHORIBOSYLTRANSFERASE
    Chains: A
    EC Number: 2.4.2.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: EF2626
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 226185
    Strain: V583

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 22)

Asymmetric Unit (5, 22)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2FMT1Ligand/IonFORMIC ACID
3GOL12Ligand/IonGLYCEROL
4MLA3Ligand/IonMALONIC ACID
5PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (4, 36)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FMT2Ligand/IonFORMIC ACID
3GOL24Ligand/IonGLYCEROL
4MLA6Ligand/IonMALONIC ACID
5PO44Ligand/IonPHOSPHATE ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:225 , ARG A:226 , ASP A:227 , HOH A:725 , HOH A:726BINDING SITE FOR RESIDUE PO4 A 501
02AC2SOFTWAREPHE A:160 , ASN A:293 , ASP A:294 , GLY A:316 , THR A:317 , HOH A:630 , HOH A:654 , HOH A:722 , HOH A:723BINDING SITE FOR RESIDUE PO4 A 502
03AC3SOFTWARETYR A:179 , ILE A:180 , GLY A:181 , GLY A:182 , LYS A:437 , LEU A:444 , HOH A:685BINDING SITE FOR RESIDUE GOL A 503
04AC4SOFTWAREGLU A:104 , TYR A:428 , PRO A:431 , TYR A:439 , HOH A:666BINDING SITE FOR RESIDUE GOL A 504
05AC5SOFTWAREMET A:396 , HIS A:398 , LYS A:406 , PRO A:461 , ASP A:463 , GOL A:513BINDING SITE FOR RESIDUE GOL A 505
06AC6SOFTWARESER A:150 , ARG A:453 , ASP A:454 , LEU A:455BINDING SITE FOR RESIDUE GOL A 506
07AC7SOFTWAREASP A:236 , LEU A:238 , LYS A:239 , HOH A:658BINDING SITE FOR RESIDUE GOL A 507
08AC8SOFTWAREASP A:85 , GLN A:364 , TRP A:384 , GLU A:386 , ASP A:387 , ARG A:389BINDING SITE FOR RESIDUE GOL A 508
09AC9SOFTWAREGLY A:212 , ASN A:213 , LEU A:486 , HOH A:631 , HOH A:758BINDING SITE FOR RESIDUE GOL A 509
10BC1SOFTWARELYS A:149 , ASP A:154 , ASP A:184BINDING SITE FOR RESIDUE GOL A 510
11BC2SOFTWAREASP A:7 , GLU A:57 , ASN A:61 , ILE A:194 , MLA A:516 , HOH A:690 , HOH A:732BINDING SITE FOR RESIDUE GOL A 511
12BC3SOFTWARELEU A:63 , GLU A:64 , LEU A:66 , GLU A:94 , PHE A:95 , LYS A:255BINDING SITE FOR RESIDUE GOL A 512
13BC4SOFTWARETYR A:270 , HIS A:398 , LYS A:459 , TYR A:460 , PRO A:461 , VAL A:462 , ASP A:463 , GOL A:505 , HOH A:673 , HOH A:701BINDING SITE FOR RESIDUE GOL A 513
14BC5SOFTWAREASP A:155 , ILE A:310 , ASP A:311BINDING SITE FOR RESIDUE GOL A 514
15BC6SOFTWAREGLN A:125 , GLU A:128 , ALA A:204 , HIS A:205 , SER A:206 , LYS A:333 , FMT A:520 , HOH A:626 , HOH A:721BINDING SITE FOR RESIDUE MLA A 515
16BC7SOFTWAREASP A:7 , ARG A:58 , ASP A:169 , TRP A:173 , ARG A:190 , GOL A:511 , HOH A:759BINDING SITE FOR RESIDUE MLA A 516
17BC8SOFTWAREGLU A:38 , TYR A:40 , PRO A:113 , THR A:359 , LYS A:363 , HOH A:714 , HOH A:730 , HOH A:761BINDING SITE FOR RESIDUE MLA A 517
18BC9SOFTWAREARG A:163 , ARG A:164 , VAL A:331 , PHE A:332BINDING SITE FOR RESIDUE CL A 518
19CC1SOFTWAREARG A:274BINDING SITE FOR RESIDUE CL A 519
20CC2SOFTWAREPHE A:160 , ARG A:262 , MLA A:515BINDING SITE FOR RESIDUE FMT A 520
21CC3SOFTWARETHR A:202 , HOH A:638 , HOH A:768 , HOH A:769BINDING SITE FOR RESIDUE CL A 521
22CC4SOFTWARESER A:200 , GLY A:201 , HOH A:767 , HOH A:768BINDING SITE FOR RESIDUE CL A 522

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MZY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MZY)

(-) 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:486
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4mzya1 A:3-140 Putative nicotinate phosphoribosyltransferase EF2626                                                                      d4mzya2 A:141-488 Putative nicotinate phosphoribosyltransferase EF2626                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhh.....eeeeeee...hhhhh..ee..hhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhh.....eeee.....ee......eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhhhhhhheeeeeee...hhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhh.....eeeehhhhhh.........eeeeeeee.....eee................eeeeeeee.....eeeeeeee...hhhhh.eeeee.......eeeee.eeeee..eeeee..ee.....hhhhhhhhhhhhhhhhhhhhhh........eeehhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mzy A   3 YTYADDSLTLHTDMYQINMMQTYWELGRADLHAVFECYFREMPFNHGYAIFAGLERLVNYLENLTFTESDIAYLREVEEYPEDFLTYLANFEFKCTVRSALEGDLVFNNEPLIQIEGPLAQCQLVETALLNMVNFQTLIATKAARIKSVIGDDPLLEFGTRRAQELDAAIWGTRAAYIGGADATSNVRAGKIFGIPVSGTHAHSLVQSYGNDYEAFMAYAKTHRDCVFLVDTYDTLKAGVPSAIRVAREMGDKINFLGVRIDSGDMAYISKRVREQLDEAGFTEAKIYASNDLDENTILNLKMQKSKIDVWGVGTKLITAYDQPALGAVFKLVSIEGEDGQMKDTIKLSSNAEKVTTPGKKQVWRITRKSDKKSEGDYVTLWNEDPRQEEEIYMFHPVHTFINKYVRDFEARPVLQDIFVEGKRVYELPTLDEIKQYAKENLDSLHEEYKRDLNPQKYPVDLSTDCWNHKMNLLEKVRKDVKHLTE 488
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482
   Legend:   → Mismatch (orange background)
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    → 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, 2)

Asymmetric 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 4MZY)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        Q830Y8_ENTFA | Q830Y8: 2f7f

(-) Related Entries Specified in the PDB File

2f7f THE SAME PROTEIN, COMPLEX WITH NICOTINIC ACID AND DIPHOSPHATE RELATED ID: NYSGXRC-6261B RELATED DB: TARGETTRACK