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(-) Description

Title :  X-RAY STRUCTURE OF A BETA-CARBONIC ANHYDRASE FROM THE RED ALGA, PORPHYRIDIUM PURPUREUM R-1
 
Authors :  S. Mitsuhashi, T. Mizushima, E. Yamashita, S. Miyachi, T. Tsukihara
Date :  12 Nov 99  (Deposition) - 08 Mar 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta-Alpha, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Mitsuhashi, T. Mizushima, E. Yamashita, M. Yamamoto, T. Kumasaka, H. Moriyama, T. Ueki, S. Miyachi, T. Tsukihara
X-Ray Structure Of Beta-Carbonic Anhydrase From The Red Alga, Porphyridium Purpureum, Reveals A Novel Catalytic Site For Co(2) Hydration.
J. Biol. Chem. V. 275 5521 2000
PubMed-ID: 10681531  |  Reference-DOI: 10.1074/JBC.275.8.5521
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBONIC ANHYDRASE
    Chains: A, B
    EC Number: 4.2.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PORPHYRIDIUM PURPUREUM
    Organism Taxid: 35688
    Variant: R-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:149 , ASP A:151 , HIS A:205 , CYS A:208 , GLY A:209BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWARECYS A:403 , ASP A:405 , HIS A:459 , CYS A:462BINDING SITE FOR RESIDUE ZN A 2
3AC3SOFTWARECYS B:149 , ASP B:151 , HIS B:205 , CYS B:208BINDING SITE FOR RESIDUE ZN B 3
4AC4SOFTWARECYS B:403 , ASP B:405 , HIS B:459 , CYS B:462BINDING SITE FOR RESIDUE ZN B 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DDZ)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DDZ)

(-) 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:481
 aligned with Q43060_PORPP | Q43060 from UniProtKB/TrEMBL  Length:571

    Alignment length:481
                                    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       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563 
         Q43060_PORPP    84 VMSDLEKKFIELEAKLVAQPAGQAMPGKSNIFANNEAWRQEMLKQDPEFFNRLANGQSPEYLWIGCADSRVPANQLLDLPAGEVFVHRNIANQCIHSDISFLSVLQYAVQYLKVKHILVCGHYGCGGAKAALGDSRLGLIDNWLRHIRDVRRMNAKYLDKCKDGDEELNRLIELNVLEQVHNVCATSIVQDAWDAGQELTVQGVVYGVGDGKLRDLGVVVNSSDDISKFYRTKSDSGALKAGNPNAPLVQVTKGGESELDSTMEKLTAELVQQTPGKLKEGANRVFVNNENWRQKMLKQDPQFFSNLAHTQTPEILWIGCADSRVPANQIINLPAGEVFVHRNIANQCIHSDMSFLSVLQYAVQYLKVKRVVVCGHYACGGCAAALGDSRLGLIDNWLRHIRDVRRHNQAELSRITDPKDSLNRLIEINVLEQMHNVCATSIVQDAWDAGQELEVQGVVYGVGDGKLRDMGVVAKANDDIG 564
               SCOP domains d1ddza1 A:84-325 beta-carbonic anhydrase                                                                                                                                                                                                          d1ddza2 A:326-564 beta-carbonic anhydrase                                                                                                                                                                                                       SCOP domains
               CATH domains 1ddzA01 A:84-139,A:394-564                              1ddzA02 A:140-307,A:339-393 Beta-carbonic Anhydrase; Chain A                                                                                                            -------------------------------1ddzA02 A:140-307,A:339-393                            1ddzA01 A:84-139,A:394-564 Beta-carbonic Anhydrase; Chain A                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhh.....eeeeee.....hhhhhh......eeeeeehhhh....hhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.......eeeeee......hhhhh..........................hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhh......eeeeee.....hhhhhh......eeeeee........hhhhhhhhhhhhhh....eeeeeee..hhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.......eeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ddz A  84 VMSDLEKKFIELEAKLVAQPAGQAMPGKSNIFANNEAWRQEMLKQDPEFFNRLANGQSPEYLWIGCADSRVPANQLLDLPAGEVFVHRNIANQCIHSDISFLSVLQYAVQYLKVKHILVCGHYGCGGAKAALGDSRLGLIDNWLRHIRDVRRMNAKYLDKCKDGDEELNRLIELNVLEQVHNVCATSIVQDAWDAGQELTVQGVVYGVGDGKLRDLGVVVNSSDDISKFYRTKSDSGALKAGNPNAPLVQVTKGGESELDSTMEKLTAELVQQTPGKLKEGANRVFVNNENWRQKMLKQDPQFFSNLAHTQTPEILWIGCADSRVPANQIINLPAGEVFVHRNIANQCIHSDMSFLSVLQYAVQYLKVKRVVVCGHYACGGCAAALGDSRLGLIDNWLRHIRDVRRHNQAELSRITDPKDSLNRLIEINVLEQMHNVCATSIVQDAWDAGQELEVQGVVYGVGDGKLRDMGVVAKANDDIG 564
                                    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       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563 


Chain B from PDB  Type:PROTEIN  Length:481
 aligned with Q43060_PORPP | Q43060 from UniProtKB/TrEMBL  Length:571

    Alignment length:481
                                    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       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563 
         Q43060_PORPP    84 VMSDLEKKFIELEAKLVAQPAGQAMPGKSNIFANNEAWRQEMLKQDPEFFNRLANGQSPEYLWIGCADSRVPANQLLDLPAGEVFVHRNIANQCIHSDISFLSVLQYAVQYLKVKHILVCGHYGCGGAKAALGDSRLGLIDNWLRHIRDVRRMNAKYLDKCKDGDEELNRLIELNVLEQVHNVCATSIVQDAWDAGQELTVQGVVYGVGDGKLRDLGVVVNSSDDISKFYRTKSDSGALKAGNPNAPLVQVTKGGESELDSTMEKLTAELVQQTPGKLKEGANRVFVNNENWRQKMLKQDPQFFSNLAHTQTPEILWIGCADSRVPANQIINLPAGEVFVHRNIANQCIHSDMSFLSVLQYAVQYLKVKRVVVCGHYACGGCAAALGDSRLGLIDNWLRHIRDVRRHNQAELSRITDPKDSLNRLIEINVLEQMHNVCATSIVQDAWDAGQELEVQGVVYGVGDGKLRDMGVVAKANDDIG 564
               SCOP domains d1ddzb1 B:84-325 beta-carbonic anhydrase                                                                                                                                                                                                          d1ddzb2 B:326-564 beta-carbonic anhydrase                                                                                                                                                                                                       SCOP domains
               CATH domains 1ddzB01 B:84-139,B:394-564                              1ddzB02 B:140-307,B:339-393 Beta-carbonic Anhydrase; Chain A                                                                                                            -------------------------------1ddzB02 B:140-307,B:339-393                            1ddzB01 B:84-139,B:394-564 Beta-carbonic Anhydrase; Chain A                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhh.....eeeeee.....hhhhhh......eeeeeehhhh....hhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.......eeeeee......hhhhh..........................hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhh......eeeeee.....hhhhhh......eeeeee........hhhhhhhhhhhhhh....eeeeeee..hhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee.......eeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ddz B  84 VMSDLEKKFIELEAKLVAQPAGQAMPGKSNIFANNEAWRQEMLKQDPEFFNRLANGQSPEYLWIGCADSRVPANQLLDLPAGEVFVHRNIANQCIHSDISFLSVLQYAVQYLKVKHILVCGHYGCGGAKAALGDSRLGLIDNWLRHIRDVRRMNAKYLDKCKDGDEELNRLIELNVLEQVHNVCATSIVQDAWDAGQELTVQGVVYGVGDGKLRDLGVVVNSSDDISKFYRTKSDSGALKAGNPNAPLVQVTKGGESELDSTMEKLTAELVQQTPGKLKEGANRVFVNNENWRQKMLKQDPQFFSNLAHTQTPEILWIGCADSRVPANQIINLPAGEVFVHRNIANQCIHSDMSFLSVLQYAVQYLKVKRVVVCGHYACGGCAAALGDSRLGLIDNWLRHIRDVRRHNQAELSRITDPKDSLNRLIEINVLEQMHNVCATSIVQDAWDAGQELEVQGVVYGVGDGKLRDMGVVAKANDDIG 564
                                    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       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q43060_PORPP | Q43060)
molecular function
    GO:0004089    carbonate dehydratase activity    Catalysis of the reaction: H2CO3 = CO2 + H2O.
    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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0015976    carbon utilization    A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary carbon sources and then activates genes to scavenge the last traces of the primary carbon source and to transport and metabolize alternative carbon sources such as carbon dioxide or carbonic acid. The utilization process begins when the cell or organism detects carbon levels, includes the activation of genes whose products detect, transport or metabolize carbon-containing substances, and ends when carbon is incorporated into the cell or organism's metabolism.

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