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(-) Description

Title :  CRYSTAL STRUCTURE OF N-ACETYLGALACTOSAMINIDASE IN COMPLEX WITH GALNAC
 
Authors :  G. Sulzenbacher, Q. P. Liu, Y. Bourne, B. Henrissat, H. Clausen
Date :  07 Jul 06  (Deposition) - 10 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  N-Acetylgalactosaminidase, Nad, A-Eco Conversion, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. P. Liu, G. Sulzenbacher, H. Yuan, E. P. Bennett, G. Pietz, K. Saunders, J. Spence, E. Nudelman, S. B. Levery, T. White, J. M. Neveu, W. S. Lane, Y. Bourne, M. L. Olsson, B. Henrissat, H. Clausen
Bacterial Glycosidases For The Production Of Universal Red Blood Cells.
Nat. Biotechnol. V. 25 454 2007
PubMed-ID: 17401360  |  Reference-DOI: 10.1038/NBT1298

(-) Compounds

Molecule 1 - ALPHA-N-ACETYLGALACTOSAMINIDASE
    Atcc: 13253
    Chains: A
    EC Number: 3.2.1.49
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Variant: PLYSS
    Expression System Vector: PET28
    Organism Scientific: FLAVOBACTERIUM MENINGOSEPTICUM
    Organism Taxid: 238

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
1A2G2Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MRD4Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:151 , TYR A:179 , HIS A:181 , ARG A:213 , TYR A:225 , HIS A:228 , TYR A:307 , NAD A:1445 , HOH A:2177BINDING SITE FOR RESIDUE A2G A1446
2AC2SOFTWAREALA A:27 , GLY A:29 , LEU A:30 , ARG A:31 , ALA A:51 , ASP A:52 , PRO A:53 , ASP A:54 , MET A:57 , ASN A:80 , SER A:98 , SER A:99 , PRO A:100 , TRP A:101 , TRP A:103 , HIS A:104 , HIS A:107 , GLU A:121 , VAL A:122 , ASN A:150 , SER A:208 , GLU A:209 , TRP A:212 , TYR A:225 , HIS A:228 , A2G A:1446 , HOH A:2014 , HOH A:2020 , HOH A:2175BINDING SITE FOR RESIDUE NAD A1445
3AC3SOFTWAREGLU A:391 , ALA A:392 , PRO A:394 , THR A:437 , TYR A:444BINDING SITE FOR RESIDUE MRD A1447
4AC4SOFTWARELYS A:350 , TRP A:351 , TYR A:355BINDING SITE FOR RESIDUE MRD A1448
5AC5SOFTWARESER A:138 , GLU A:139 , GLY A:142 , PRO A:144 , VAL A:397 , TYR A:398 , HOH A:2178BINDING SITE FOR RESIDUE MPD A1449

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IXB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IXB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IXB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IXB)

(-) Exons   (0, 0)

(no "Exon" information available for 2IXB)

(-) 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:426
 aligned with GH109_ELIME | A4Q8F7 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:426
                                    28        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       328       338       348       358       368       378       388       398       408       418       428       438      
          GH109_ELIME    19 KKVRIAFIAVGLRGQTHVENMARRDDVEIVAFADPDPYMVGRAQEILKKNGKKPAKVFGNGNDDYKNMLKDKNIDAVFVSSPWEWHHEHGVAAMKAGKIVGMEVSGAITLEECWDYVKVSEQTGVPLMALENVCYRRDVMAILNMVRKGMFGELVHGTGGYQHDLRPVLFNSGINGKNGDGVEFGEKAFSEAKWRTNHYKNRNGELYPTHGVGPLHTMMDINRGNRLLRLSSFASKARGLHKYIVDKGGESHPNAKVEWKQGDIVTTQIQCHNGETIVLTHDTSLQRPYNLGFKVQGTEGLWEDFGWGEAAQGFIYFEKIMNHSHRWDSSEKWIKEYDHPMWKKHEQKAVGAGHGGMDYFLDNTFVECIKRNEAFPLDVYDLATWYSITPLSEKSIAENGAVQEIPDFTNGKWKNAKNTFAINDDY 444
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhh.....eee.....hhhhhhh.....eeee...hhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhh...eee...hhh.hhhhhhhhhhhh......eeeeeeee...hhhhh....................hhhhhhhhhhhh......hhhhhhhhhhh........eeeeeee...hhhhhhhhhhh.....hhh........eeeeeee....eeeeeee...........eeee...eeee........eeee..............hhhhhhh..hhhhhhhhhh......hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.............hhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ixb A  19 KKVRIAFIAVGLRGQTHVENMARRDDVEIVAFADPDPYMVGRAQEILKKNGKKPAKVFGNGNDDYKNMLKDKNIDAVFVSSPWEWHHEHGVAAMKAGKIVGMEVSGAITLEECWDYVKVSEQTGVPLMALENVCYRRDVMAILNMVRKGMFGELVHGTGGYQHDLRPVLFNSGINGKNGDGVEFGEKAFSEAKWRTNHYKNRNGELYPTHGVGPLHTMMDINRGNRLLRLSSFASKARGLHKYIVDKGGESHPNAKVEWKQGDIVTTQIQCHNGETIVLTHDTSLQRPYNLGFKVQGTEGLWEDFGWGEAAQGFIYFEKIMNHSHRWDSSEKWIKEYDHPMWKKHEQKAVGAGHGGMDYFLDNTFVECIKRNEAFPLDVYDLATWYSITPLSEKSIAENGAVQEIPDFTNGKWKNAKNTFAINDDY 444
                                    28        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       328       338       348       358       368       378       388       398       408       418       428       438
   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  (0, 0)

(no "SCOP Domain" information available for 2IXB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2IXB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IXB)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (GH109_ELIME | A4Q8F7)
molecular function
    GO:0008456    alpha-N-acetylgalactosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-alpha-D-galactosaminides.
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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(-) Related Entries Specified in the PDB File

2ixa A-ZYME, N-ACETYLGALACTOSAMINIDASE