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(-) Description

Title :  ALGINATE LYASE A1-III Y246F COMPLEXED WITH TETRASACCHARIDE
 
Authors :  B. Mikami, M. Ban, S. Suzuki, H. -J. Yoon, O. Miyake, M. Yamasaki, K. Ogur Y. Maruyama, W. Hashimoto, K. Murata
Date :  06 May 12  (Deposition) - 27 Jun 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha Barrel, Polysaccharide Lyase, Alginate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Mikami, M. Ban, S. Suzuki, H. -J. Yoon, O. Miyake, M. Yamasaki, K. Ogura, Y. Maruyama, W. Hashimoto, K. Murata
Induced-Fit Motion Of A Lid Loop Involved In Catalysis In Alginate Lyase A1-Iii
Acta Crystallogr. , Sect. D V. 68 1207 2012
PubMed-ID: 22948922  |  Reference-DOI: 10.1107/S090744491202495X

(-) Compounds

Molecule 1 - ALGINATE LYASE
    Chains: A, B
    EC Number: 4.2.2.3
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Plasmid: PISA412
    Expression System Taxid: 1423
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 54-404
    Gene: ALY
    Mutation: YES
    Organism Scientific: SPHINGOMONAS
    Organism Taxid: 28214
    Strain: A1
    Synonym: ALGINATE LYASE A1-III

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1BEM5Ligand/IonBETA-D-MANNURONIC ACID
2MAW1Ligand/Ion4-DEOXY-ALPHA-L-ERYTHRO-HEX-4-ENOPYRANURONIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1BEM3Ligand/IonBETA-D-MANNURONIC ACID
2MAW1Ligand/Ion4-DEOXY-ALPHA-L-ERYTHRO-HEX-4-ENOPYRANURONIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1BEM2Ligand/IonBETA-D-MANNURONIC ACID
2MAW-1Ligand/Ion4-DEOXY-ALPHA-L-ERYTHRO-HEX-4-ENOPYRANURONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:67 , TYR A:68 , TYR A:80 , ARG A:88 , GLN A:134 , TYR A:137 , TRP A:141 , ASN A:191 , HIS A:192 , ARG A:239 , HIS A:245 , PHE A:246 , TYR A:249 , ARG A:306 , ARG A:312 , GLY A:313 , ARG A:342 , HOH A:503 , HOH A:507 , HOH A:514 , HOH A:516 , HOH A:526 , HOH A:540 , HOH A:572 , HOH A:588 , HOH A:630BINDING SITE FOR LINKED RESIDUES A 401 TO 404
2AC2SOFTWAREARG B:88 , TRP B:141 , HIS B:245 , TYR B:249 , ARG B:306 , ARG B:312 , ARG B:342 , HOH B:511 , HOH B:542 , HOH B:591 , HOH B:619BINDING SITE FOR LINKED RESIDUES B 401 TO 402

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:49 -A:112
2A:188 -A:189
3B:49 -B:112
4B:188 -B:189

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F13)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F13)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F13)

(-) Exons   (0, 0)

(no "Exon" information available for 4F13)

(-) 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:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4f13a_ A: Alginate lyase A1-III                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhh..hhhhhhhh....hhhhh..........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhh.............hhhhh.hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f13 A   5 SHPFDQAVVKDPTASYVDVKARRTFLQSGQLDDRLKAALPKEYDCTTEATPNPQQGEMVIPRRYLSGNHGPVNPDYEPVVTLYRDFEKISATLGNLYVATGKPVYATCLLNMLDKWAKADALLNYDPKSQSWYQVEWSAATAAFALSTMMAEPNVDTAQRERVVKWLNRVARHQTSFPGGDTSCCNNHSYWRGQEATIIGVISKDDELFRWGLGRYVQAMGLINEDGSFVHEMTRHEQSLHFQNYAMLPLTMIAETASRQGIDLYAYKENGRDIHSARKFVFAAVKNPDLIKKYASEPQDTRAFKPGRGDLNWIEYQRARFGFADELGFMTVPIFDPRTGGSATLLAYKPQG 356
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354  


Chain B from PDB  Type:PROTEIN  Length:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4f13b_ B: Alginate lyase A1-III                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhh...hhhhhhhh....hhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhh.............hhhhh.hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f13 B   5 SHPFDQAVVKDPTASYVDVKARRTFLQSGQLDDRLKAALPKEYDCTTEATPNPQQGEMVIPRRYVNPDYEPVVTLYRDFEKISATLGNLYVATGKPVYATCLLNMLDKWAKADALLNYDPKSQSWYQVEWSAATAAFALSTMMAEPNVDTAQRERVVKWLNRVARHQTSFPGGDTSCCNNHSYWRGQEATIIGVISKDDELFRWGLGRYVQAMGLINEDGSFVHEMTRHEQSLHFQNYAMLPLTMIAETASRQGIDLYAYKENGRDIHSARKFVFAAVKNPDLIKKYASEPQDTRAFKPGRGDLNWIEYQRARFGFADELGFMTVPIFDPRTGGSATLLAYKPQG 356
                                    14        24        34        44        54        64   ||   81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351     
                                                                                          68|                                                                                                                                                                                                                                                                                        
                                                                                           76
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F13)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F13)

(-) Gene Ontology  (2, 2)

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  4.2.2.3
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        Q9KWU1_SPHSX | Q9KWU1: 1hv6 1qaz 4e1y 4f10

(-) Related Entries Specified in the PDB File

4e1y H192A APO FORM
4f10 H192A/TETRASACCHARIDE COMPLEX