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(-) Description

Title :  CRYSTAL STRUCTURE OF ALGINATE LYASE A1-III COMPLEXED WITH TRISACCHARIDE PRODUCT.
 
Authors :  H. -J. Yoon, W. Hashimoto, O. Miyake, K. Murata, B. Mikami
Date :  08 Jan 01  (Deposition) - 02 May 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Alginate Lyase, Trisaccharide Complex, Alpha Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Yoon, W. Hashimoto, O. Miyake, K. Murata, B. Mikami
Crystal Structure Of Alginate Lyase A1-Iii Complexed With Trisaccharide Product At 2. 0 A Resolution.
J. Mol. Biol. V. 307 9 2001
PubMed-ID: 11243798  |  Reference-DOI: 10.1006/JMBI.2000.4509
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALGINATE LYASE
    Chains: A
    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: RESIDUE 52-402
    Organism Scientific: SPHINGOMONAS SP.
    Organism Taxid: 28214

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1GCU1Ligand/IonD-GLUCURONIC ACID
2MAV1Ligand/IonALPHA-D-MANNOPYRANURONIC ACID
3MAW1Ligand/Ion4-DEOXY-ALPHA-L-ERYTHRO-HEX-4-ENOPYRANURONIC ACID
4SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:312 , GLY A:313 , MAV A:402 , HOH A:636 , HOH A:643 , HOH A:688BINDING SITE FOR RESIDUE MAW A 401
2AC2SOFTWAREARG A:306 , ARG A:312 , MAW A:401 , GCU A:403 , HOH A:634 , HOH A:635 , HOH A:636 , HOH A:744BINDING SITE FOR RESIDUE MAV A 402
3AC3SOFTWAREARG A:88 , TRP A:141 , HIS A:245 , TYR A:246 , TYR A:249 , ARG A:342 , MAV A:402 , HOH A:635 , HOH A:640 , HOH A:641 , HOH A:655 , HOH A:717BINDING SITE FOR RESIDUE GCU A 403
4AC4SOFTWAREGLY A:184 , ASP A:185 , THR A:186 , SER A:187 , HOH A:706BINDING SITE FOR RESIDUE SO4 A 801

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:49 -A:112
2A:188 -A:189

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HV6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HV6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HV6)

(-) Exons   (0, 0)

(no "Exon" information available for 1HV6)

(-) 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:351
 aligned with Q9KWU1_SPHSX | Q9KWU1 from UniProtKB/TrEMBL  Length:641

    Alignment length:351
                                    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 QAHPFDQAVVKDPTASYVDVKARRTFLQSGQLDDRLKAALPKEYDCTTEATPNPQQGEMVIPRRYLSGNHGPVNPDYEPVVTLYRDFEKISATLGNLYVATGKPVYATCLLNMLDKWAKADALLNYDPKSQSWYQVEWSAATAAFALSTMMAEPNVDTAQRERVVKWLNRVARHQTSFPGGDTSCCNNHSYWRGQEATIIGVISKDDELFRWGLGRYVQAMGLINEDGSFVHEMTRHEQSLHYQNYAMLPLTMIAETASRQGIDLYAYKENGRDIHSARKFVFAAVKNPDLIKKYASEPQDTRAFKPGRGDLNWIEYQRARFGFADELGFMTVPIFDPRTGGSGTLLAYKP 402
               SCOP domains d1hv6a_ A: Alginate lyase A1-III                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1hv6A00 A:4-354  [code=1.50.10.110, no name defined]                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhh..hhhhhhhh....hhhhh..........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhh..............hhhh.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hv6 A   4 GSHPFDQAVVKDPTASYVDVKARRTFLQSGQLDDRLKAALPKEYDCTTEATPNPQQGEMVIPRRYLSGNHGPVNPDYEPVVTLYRDFEKISATLGNLYVATGKPVYATCLLNMLDKWAKADALLNYDPKSQSWYQVEWSAATAAFALSTMMAEPNVDTAQRERVVKWLNRVARHQTSFPGGDTSCCNNHSYWRGQEATIIGVISKDDELFRWGLGRYVQAMGLINEDGSFVHEMTRHEQSLHYQNYAMLPLTMIAETASRQGIDLYAYKENGRDIHSARKFVFAAVKNPDLIKKYASEPQDTRAFKPGRGDLNWIEYQRARFGFADELGFMTVPIFDPRTGGSATLLAYKP 354
                                    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)
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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, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HV6)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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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  4.2.2.3
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 Related Entries

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

UniProtKB/TrEMBL
        Q9KWU1_SPHSX | Q9KWU1: 1qaz 4e1y 4f10 4f13

(-) Related Entries Specified in the PDB File

1qaz 1QZA CONTAINS THE SAME PROTEIN IN APO FORM.