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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PECTIN METHYLESTERASE FROM ASPERGILLUS NIGER IN PENULTIMATELY DEGLYCOSYLATED FORM (N-ACETYLGLUCOSAMINE STUB AT ASN84)
 
Authors :  G. B. Jameson, M. A. K. Williams, T. S. Loo, L. M. Kent, L. D. Melton, D. Mer
Date :  13 Jun 15  (Deposition) - 01 Jul 15  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Parallel Beta Helix, Pectin Methylesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Kent, T. S. Loo, L. D. Melton, D. Mercadante, M. A. Williams, G. B. Jameson
Structure And Properties Of A Non-Processive, Salt-Requiring, And Acidophilic Pectin Methylesterase From Aspergillus Niger Provide Insights Into The Key Determinant Of Processivity Control.
J. Biol. Chem. V. 291 1289 2016
PubMed-ID: 26567911  |  Reference-DOI: 10.1074/JBC.M115.673152
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PECTINESTERASE
    Atcc: ATCC 11414
    Chains: A
    EC Number: 3.1.1.11
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Plasmid: PYES2
    Expression System Strain: INVSC1
    Expression System Taxid: 4932
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL TRUNCATED EXPORTED PROTEIN
    Gene: ASPNIDRAFT_214857
    Organism Scientific: ASPERGILLUS NIGER (STRAIN ATCC 1015 / CBS 113.46 / FGSC A1144 / LSHB AC4 / NCTC 3858A / NRRL 328 / USDA 3528.7)
    Organism Taxid: 380704
    Other Details: N-ACETYLGLUCOSAMINE STUB AT ASN84 (ABOVE SEQUENCE)
    Strain: VAN TIEGHEM, ANAMORPH

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3GOL5Ligand/IonGLYCEROL
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO45Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:63 , ASN A:84 , GLN A:155 , ASP A:321 , TRP A:322 , HOH A:501 , HOH A:503 , HOH A:504 , HOH A:505 , HOH A:508 , HOH A:510 , HOH A:533 , HOH A:543 , HOH A:697 , HOH A:770binding site for residue NAG A 401
02AC2SOFTWARETYR A:178 , TRP A:198 , GLY A:200 , LYS A:311 , HOH A:609 , HOH A:616 , HOH A:644binding site for residue SO4 A 402
03AC3SOFTWARETRP A:251 , ARG A:252 , HOH A:532binding site for residue SO4 A 403
04AC4SOFTWAREARG A:217 , ASP A:222 , SER A:223 , ARG A:256 , HOH A:527 , HOH A:564binding site for residue SO4 A 404
05AC5SOFTWAREPRO A:111 , GLU A:218 , ARG A:252binding site for residue SO4 A 405
06AC6SOFTWARELYS A:98 , THR A:219 , SER A:220 , SER A:221 , HOH A:552 , HOH A:628binding site for residue SO4 A 406
07AC7SOFTWAREASN A:152 , LYS A:173binding site for residue CL A 407
08AC8SOFTWAREGLN A:145 , ASP A:168 , ASP A:189 , TRP A:251 , MET A:276 , HOH A:531binding site for residue GOL A 408
09AC9SOFTWARESER A:115 , ASP A:117 , LYS A:118 , HOH A:502 , HOH A:506 , HOH A:514binding site for residue GOL A 409
10AD1SOFTWARETHR A:312 , GLU A:317 , TRP A:319 , GLY A:320 , HOH A:507binding site for residue GOL A 410
11AD2SOFTWARESER A:36 , HOH A:511 , HOH A:652binding site for residue GOL A 411
12AD3SOFTWAREARG A:249 , MET A:276binding site for residue ACT A 412
13AD4SOFTWARESER A:290 , GLY A:291 , HOH A:690binding site for residue GOL A 413

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:38 -A:65

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5C1E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C1E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C1E)

(-) Exons   (0, 0)

(no "Exon" information available for 5C1E)

(-) 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:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.......hhhhhhhhhh.....eeeee..eeee..eee.....eeeee............eeeee..hhhhhh.hhhhh.eee.....eee..eeee..........eeee...eeee..eee.....eeeee.eeeee..eeee....eee..eeeee..eeee...eeeeee..........eeee..eeee.........eeee.......eeeee..ee..................eeeee......................hhhhhhh.hhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c1e A  29 ESRTSAPSGCLTVGSDGTYSTIGDALDALGSSTSSACIYVASGTYEEQLTIDYAGNLTLYGETTDTSTYKDNVVTITHTISSPDAGSLDKSATVNVVSDGFSMYNINVENGYGEGAQAVALVGNADQLGFYGCQFSGYQDTLYVKAGTQYYSNCMIEGAVDYIFGDASVWFGECDIVSNGAGAITASSRETSSDSGWYAIDNCNIKAASGVSLTEEVYLGRPWRVLARVIYQNSVLSDIINPKGWTTMADGATPLYYEYNNSGAGSDTSDREYETSISAAVDKTTVLGETWGDWIDRSY 327
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318
   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 5C1E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C1E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C1E)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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(-) Related Entries Specified in the PDB File

5c1c DEGLYCOSYLATED FORM OF THIS PROTEIN