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(-) Description

Title :  CRYSTAL STRUCTURE OF UDP-X DIPHOSPHATASE
 
Authors :  K. C. Duong-Ly, L. M. Amzel, S. B. Gabelli
Date :  05 Oct 12  (Deposition) - 07 Aug 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.39
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Udp-Sugar Diphosphatase, Nudix, Hydrolase, Rna Exonuclease, Pyrophosphatase, Mur Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. C. Duong-Ly, H. N. Woo, C. A. Dunn, W. Xu, A. Babic, M. J. Bessman, L. M. Amzel, S. B. Gabelli
A Udp-X Diphosphatase From Streptococcus Pneumoniae Hydrolyzes Precursors Of Peptidoglycan Biosynthesis.
Plos One V. 8 64241 2013
PubMed-ID: 23691178  |  Reference-DOI: 10.1371/JOURNAL.PONE.0064241

(-) Compounds

Molecule 1 - MUTT/NUDIX FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-24A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SP1669, SP_1669
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: TIGR4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 30)

Asymmetric/Biological Unit (6, 30)
No.NameCountTypeFull Name
1EDO11Ligand/Ion1,2-ETHANEDIOL
2GOL6Ligand/IonGLYCEROL
3PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE1Ligand/IonTRIETHYLENE GLYCOL
5SO45Ligand/IonSULFATE ION
6TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:177 , SER A:178 , GLU A:179 , LYS A:180 , PEG A:310 , HOH A:464BINDING SITE FOR RESIDUE EDO A 301
02AC2SOFTWAREASP A:5 , TYR A:9 , HOH A:632BINDING SITE FOR RESIDUE EDO A 302
03AC3SOFTWAREASP A:71 , ARG A:73 , GLN A:139 , TYR A:143 , LYS A:145 , LYS A:180 , ARG A:181 , HOH A:427 , HOH A:578 , PRO B:61BINDING SITE FOR RESIDUE TRS A 303
04AC4SOFTWAREARG A:73 , VAL A:85 , GLY A:97 , GLU A:117 , GLU A:162 , ARG A:181 , HOH A:430 , HOH A:442 , HOH A:593BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWAREARG A:86 , TRP A:191 , GLN A:192 , GLN A:195 , HIS A:197 , HOH A:413 , HOH A:616 , HOH A:617BINDING SITE FOR RESIDUE SO4 A 305
06AC6SOFTWAREGLU A:101 , TYR A:104 , LYS A:112 , LYS B:8 , ARG B:12 , HOH B:509BINDING SITE FOR RESIDUE SO4 A 306
07AC7SOFTWARELEU A:111 , LYS A:112 , GLU A:115 , LYS A:121 , ALA A:122 , HOH A:445 , HOH A:446 , HOH A:470BINDING SITE FOR RESIDUE PEG A 307
08AC8SOFTWARELYS A:8 , ASN A:134 , HOH A:420 , HOH B:571BINDING SITE FOR RESIDUE EDO A 308
09AC9SOFTWAREARG A:135 , ASP A:203 , HOH A:438 , HOH A:605 , HOH A:633 , SER B:105 , GLU B:108BINDING SITE FOR RESIDUE GOL A 309
10BC1SOFTWAREASN A:176 , LEU A:177 , GLU A:179 , LYS A:184 , EDO A:301 , HOH A:414 , HOH A:462 , HOH A:629BINDING SITE FOR RESIDUE PEG A 310
11BC2SOFTWARELYS A:2 , THR A:3 , SER A:4 , HOH A:498 , HOH A:508BINDING SITE FOR RESIDUE SO4 A 311
12BC3SOFTWAREALA A:66 , HOH A:429 , HOH A:485 , HOH A:511 , PHE B:99 , GLY B:100 , GLU B:101BINDING SITE FOR RESIDUE EDO A 312
13BC4SOFTWARETHR A:62 , SER A:63 , TYR A:65 , ALA A:66 , THR A:67 , LEU A:69 , LYS A:141 , GLN A:142 , HOH A:412 , HOH A:416 , HOH A:502 , HOH A:584 , LEU B:69 , VAL B:102BINDING SITE FOR RESIDUE PGE A 313
14BC5SOFTWARESER A:63 , VAL A:102 , HOH A:507 , ALA B:15 , LEU B:69 , LYS B:141 , GLN B:142 , HOH B:415 , HOH B:441BINDING SITE FOR RESIDUE GOL A 314
15BC6SOFTWAREGLU A:78 , PHE A:120 , LEU A:152 , PHE A:168 , HOH A:532 , HOH A:534 , HOH A:590BINDING SITE FOR RESIDUE GOL A 315
16BC7SOFTWAREASP A:91 , TRP A:93 , GLN A:167 , ASN A:176 , EDO A:317 , HOH A:408BINDING SITE FOR RESIDUE PEG A 316
17BC8SOFTWAREASP A:91 , ASN A:176 , LEU A:189 , GLN A:192 , ARG A:198 , PEG A:316 , HOH A:408BINDING SITE FOR RESIDUE EDO A 317
18BC9SOFTWAREGLN B:139 , SER B:140 , LYS B:180 , EDO B:302 , HOH B:432 , HOH B:461BINDING SITE FOR RESIDUE SO4 B 301
19CC1SOFTWAREASN B:45 , LEU B:138 , SO4 B:301 , HOH B:528 , HOH B:530BINDING SITE FOR RESIDUE EDO B 302
20CC2SOFTWAREARG B:73 , GLN B:139 , TYR B:143 , LYS B:145 , LYS B:180 , ARG B:181 , TRS B:305 , HOH B:477 , HOH B:626BINDING SITE FOR RESIDUE GOL B 303
21CC3SOFTWAREGLU B:78 , PHE B:120 , PHE B:168 , HOH B:438 , HOH B:534 , HOH B:543 , HOH B:640BINDING SITE FOR RESIDUE GOL B 304
22CC4SOFTWAREARG B:73 , GLY B:97 , GLU B:117 , GLU B:162 , ILE B:163 , ARG B:181 , GOL B:303 , HOH B:439 , HOH B:477 , HOH B:596 , HOH B:633BINDING SITE FOR RESIDUE TRS B 305
23CC5SOFTWAREPRO A:68 , LEU A:69 , MET A:70 , THR A:144 , PRO B:68 , MET B:70 , THR B:144 , PHE B:146 , HOH B:544BINDING SITE FOR RESIDUE EDO B 306
24CC6SOFTWARELYS A:123 , LEU B:177 , SER B:178 , GLU B:179 , LYS B:180 , HOH B:559 , HOH B:604 , HOH B:615BINDING SITE FOR RESIDUE TRS B 307
25CC7SOFTWAREARG A:12 , GLU B:31 , ASP B:35 , GLU B:101 , LYS B:112 , GLU B:116 , HOH B:417 , HOH B:525BINDING SITE FOR RESIDUE GOL B 308
26CC8SOFTWARELEU A:21 , THR A:22 , HOH B:446 , HOH B:618 , HOH B:620BINDING SITE FOR RESIDUE EDO B 309
27CC9SOFTWAREARG A:30 , HOH A:441 , THR B:24 , LYS B:25 , PRO B:27 , ARG B:30 , HOH B:516BINDING SITE FOR RESIDUE EDO B 310
28DC1SOFTWARELEU B:202 , PEG B:313 , HOH B:542 , HOH B:643BINDING SITE FOR RESIDUE EDO B 311
29DC2SOFTWAREARG B:86 , TRP B:93 , GLY B:196 , ARG B:198 , GLY B:199 , HOH B:428BINDING SITE FOR RESIDUE EDO B 312
30DC3SOFTWARELEU B:174 , PRO B:175 , ARG B:198 , GLY B:199 , GLN B:200 , TYR B:201 , LEU B:202 , EDO B:311 , HOH B:440 , HOH B:567BINDING SITE FOR RESIDUE PEG B 313

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys B:60 -Pro B:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HFQ)

(-) 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:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh........eeeeeee.ee..eeeeeee.....ee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeeeehhhhh.....eeeeeeeeeeeee.......eeeeeeee............hhhhhhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hfq A   1 MKTSDFVKYLQRMIAITDTGLTFTKDPFDRERYEDLRSLLSEMLNQASDLDSEEVAEVLKPTSAYATPLMDVRAWIVEDEKICLVRGQGEDSWALPGGFGEVGYSPTENILKEIEEETGFKAKVERLLAVFDTNRFQLQSKQYTKFVFGCKLLDGQFQENQEIADLQFFAIDQLPNLSEKRITKEQIELLWQVYQGHRGQYLD 203
                                    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:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh........eeeeeee.ee..eeeeeee.....ee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeeeehhhhh.....eeeeeeeeeeeee.......eeeeeeehhhhh........hhhhhhhhhhhhh.....ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hfq B   1 MKTSDFVKYLQRMIAITDTGLTFTKDPFDRERYEDLRSLLSEMLNQASDLDSEEVAEVLKPTSAYATPLMDVRAWIVEDEKICLVRGQGEDSWALPGGFGEVGYSPTENILKEIEEETGFKAKVERLLAVFDTNRFQLQSKQYTKFVFGCKLLDGQFQENQEIADLQFFAIDQLPNLSEKRITKEQIELLWQVYQGHRGQYLD 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4HFQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HFQ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4HFQ)

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