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(-) Description

Title :  ALGINATE LYASE A1-III H192A 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 :  05 May 12  (Deposition) - 27 Jun 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha Barrel, Polysaccharide Lyase, Aliginate, 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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1BEM3Ligand/IonBETA-D-MANNURONIC ACID
2LGU2Ligand/IonALPHA-L-GULURONATE
3MAW1Ligand/Ion4-DEOXY-ALPHA-L-ERYTHRO-HEX-4-ENOPYRANURONIC ACID
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1BEM2Ligand/IonBETA-D-MANNURONIC ACID
2LGU1Ligand/IonALPHA-L-GULURONATE
3MAW1Ligand/Ion4-DEOXY-ALPHA-L-ERYTHRO-HEX-4-ENOPYRANURONIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1BEM1Ligand/IonBETA-D-MANNURONIC ACID
2LGU1Ligand/IonALPHA-L-GULURONATE
3MAW-1Ligand/Ion4-DEOXY-ALPHA-L-ERYTHRO-HEX-4-ENOPYRANURONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:67 , TYR A:80 , ARG A:88 , GLN A:134 , TYR A:137 , TRP A:141 , ASN A:190 , ASN A:191 , ARG A:239 , HIS A:245 , TYR A:246 , TYR A:249 , ARG A:306 , ARG A:312 , GLY A:313 , ARG A:342 , HOH A:534 , HOH A:550 , HOH A:552 , HOH A:554 , HOH A:557 , HOH A:558 , HOH A:559 , HOH A:561 , HOH A:634 , HOH A:651 , HOH A:658BINDING SITE FOR LINKED RESIDUES A 401 TO 404
2AC2SOFTWAREARG B:88 , TRP B:141 , HIS B:245 , TYR B:246 , TYR B:249 , ARG B:306 , ARG B:312 , ARG B:342 , HOH B:539 , HOH B:540 , HOH B:557 , HOH B:567 , HOH B:627BINDING 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  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:4 -Ser A:5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F10)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F10)

(-) Exons   (0, 0)

(no "Exon" information available for 4F10)

(-) 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:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4f10a_ A: Alginate lyase A1-III                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhh..hhhhhhhh....hhhhh..........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhh.............hhhhh.hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f10 A   4 GSHPFDQAVVKDPTASYVDVKARRTFLQSGQLDDRLKAALPKEYDCTTEATPNPQQGEMVIPRRYLSGNHGPVNPDYEPVVTLYRDFEKISATLGNLYVATGKPVYATCLLNMLDKWAKADALLNYDPKSQSWYQVEWSAATAAFALSTMMAEPNVDTAQRERVVKWLNRVARHQTSFPGGDTSCCNNASYWRGQEATIIGVISKDDELFRWGLGRYVQAMGLINEDGSFVHEMTRHEQSLHYQNYAMLPLTMIAETASRQGIDLYAYKENGRDIHSARKFVFAAVKNPDLIKKYASEPQDTRAFKPGRGDLNWIEYQRARFGFADELGFMTVPIFDPRTGGSATLLAYKPQG 356
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353   


Chain B from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4f10b_ B: Alginate lyase A1-III                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhh...hhhhhhhh....hhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhh..hhhhh.............hhhhhhhhhhhhhhh.............hhhhh.hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f10 B   4 GSHPFDQAVVKDPTASYVDVKARRTFLQSGQLDDRLKAALPKEYDCTTEATPNPQQGEMVIPDYEPVVTLYRDFEKISATLGNLYVATGKPVYATCLLNMLDKWAKADALLNYDPKSQSWYQVEWSAATAAFALSTMMAEPNVDTAQRERVVKWLNRVARHQTSFPGGDTSCCNNASYWRGQEATIIGVISKDDELFRWGLGRYVQAMGLINEDGSFVHEMTRHEQSLHYQNYAMLPLTMIAETASRQGIDLYAYKENGRDIHSARKFVFAAVKNPDLIKKYASEPQDTRAFKPGRGDLNWIEYQRARFGFADELGFMTVPIFDPRTGGSATLLAYKPQG 356
                                    13        23        33        43        53        63 ||     86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356
                                                                                        65|                                                                                                                                                                                                                                                                                     
                                                                                         79
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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 4F10)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F10)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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  Q9KWU1_SPHSX | Q9KWU1
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  4.2.2.3
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        Q9KWU1_SPHSX | Q9KWU1: 1hv6 1qaz 4e1y 4f13

(-) Related Entries Specified in the PDB File

4e1y H192A APO FORM
4e25 Y246F/TETRASACCHARIDE COMPLEX