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(-) Description

Title :  ALGINATE LYASE A1-III H192A APO FORM
 
Authors :  B. Mikami, M. Ban, S. Suzuki, H. -J. Yoon, O. Miyake, M. Yamasaki, K. Ogur Y. Maruyama, W. Hashimoto, K. Murata
Date :  07 Mar 12  (Deposition) - 11 Apr 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
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 Strain: 1423
    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

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4E1Y)

(-) Sites  (0, 0)

(no "Site" information available for 4E1Y)

(-) 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  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:4 -Ser A:5
2Gly B:4 -Ser B:5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E1Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E1Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4E1Y)

(-) 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
 aligned with Q9KWU1_SPHSX | Q9KWU1 from UniProtKB/TrEMBL  Length:641

    Alignment length:353
                                    61        71        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       361       371       381       391       401   
         Q9KWU1_SPHSX    52 QAHPFDQAVVKDPTASYVDVKARRTFLQSGQLDDRLKAALPKEYDCTTEATPNPQQGEMVIPRRYLSGNHGPVNPDYEPVVTLYRDFEKISATLGNLYVATGKPVYATCLLNMLDKWAKADALLNYDPKSQSWYQVEWSAATAAFALSTMMAEPNVDTAQRERVVKWLNRVARHQTSFPGGDTSCCNNHSYWRGQEATIIGVISKDDELFRWGLGRYVQAMGLINEDGSFVHEMTRHEQSLHYQNYAMLPLTMIAETASRQGIDLYAYKENGRDIHSARKFVFAAVKNPDLIKKYASEPQDTRAFKPGRGDLNWIEYQRARFGFADELGFMTVPIFDPRTGGSGTLLAYKPQG 404
               SCOP domains d4e1ya_ A: Alginate lyase A1-III                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhh..hhhhhhhh....hhhhh..........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhh.hhhhhh..............hhhhhhhhhhhhhhh.............hhhhh.hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e1y A   4 GSHPFDQAVVKDPTASYVDVKARRTFLQSGQLDDRLKAALPKEYDCTTEATPNPQQGEMVIPRRYLSGNHGPVNPDYEPVVTLYRDFEKISATLGNLYVATGKPVYATCLLNMLDKWAKADALLNYDPKSQSWYQVEWSAATAAFALSTMMAEPNVDTAQRERVVKWLNRVARHQTSFPGGDTSCCNNASYWRGQEATIIGVISKDDELFRWGLGRYVQAMGLINEDGSFVHEMTRHEQSLHYQNYAMLPLTMIAETASRQGIDLYAYKENGRDIHSARKFVFAAVKNPDLIKKYASEPQDTRAFKPGRGDLNWIEYQRARFGFADELGFMTVPIFDPRTGGSGTLLAYKPQG 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:353
 aligned with Q9KWU1_SPHSX | Q9KWU1 from UniProtKB/TrEMBL  Length:641

    Alignment length:353
                                    61        71        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       361       371       381       391       401   
         Q9KWU1_SPHSX    52 QAHPFDQAVVKDPTASYVDVKARRTFLQSGQLDDRLKAALPKEYDCTTEATPNPQQGEMVIPRRYLSGNHGPVNPDYEPVVTLYRDFEKISATLGNLYVATGKPVYATCLLNMLDKWAKADALLNYDPKSQSWYQVEWSAATAAFALSTMMAEPNVDTAQRERVVKWLNRVARHQTSFPGGDTSCCNNHSYWRGQEATIIGVISKDDELFRWGLGRYVQAMGLINEDGSFVHEMTRHEQSLHYQNYAMLPLTMIAETASRQGIDLYAYKENGRDIHSARKFVFAAVKNPDLIKKYASEPQDTRAFKPGRGDLNWIEYQRARFGFADELGFMTVPIFDPRTGGSGTLLAYKPQG 404
               SCOP domains d4e1yb_ B: Alginate lyase A1-III                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhh..hhhhhhhh....hhhhh..........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhh.............hhhhh.hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e1y B   4 GSHPFDQAVVKDPTASYVDVKARRTFLQSGQLDDRLKAALPKEYDCTTEATPNPQQGEMVIPRRYLSGNHGPVNPDYEPVVTLYRDFEKISATLGNLYVATGKPVYATCLLNMLDKWAKADALLNYDPKSQSWYQVEWSAATAAFALSTMMAEPNVDTAQRERVVKWLNRVARHQTSFPGGDTSCCNNASYWRGQEATIIGVISKDDELFRWGLGRYVQAMGLINEDGSFVHEMTRHEQSLHYQNYAMLPLTMIAETASRQGIDLYAYKENGRDIHSARKFVFAAVKNPDLIKKYASEPQDTRAFKPGRGDLNWIEYQRARFGFADELGFMTVPIFDPRTGGSGTLLAYKPQG 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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 2)

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

(-) CATH Domains  (0, 0 ; only for superseded entry 3EVH: 1,2)

(no "CATH Domain" information available for 4E1Y, only for superseded entry 3EVH replaced by 4E1Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E1Y)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9KWU1_SPHSX | Q9KWU1)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9KWU1_SPHSX | Q9KWU1: 1hv6 1qaz 4f10 4f13

(-) Related Entries Specified in the PDB File

4e23 H192A/TETRASACCHARIDE COMPLEX
4e25 Y246F/TETRASACCHARIDE COMPLEX