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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE CD-BOUND DOMAIN 3 OF THE CADMIUM CARBONIC ANHYDRASE FROM MARINE DIATOM THALASSIOSIRA WEISSFLOGII
 
Authors :  V. Alterio, G. De Simone
Date :  09 Nov 11  (Deposition) - 11 Jul 12  (Release) - 11 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Marine Diatom, Carbonic Anhydrase, Lyase, Cadmium-Bound, Acetate- Bound (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Alterio, E. Langella, F. Viparelli, D. Vullo, G. Ascione, N. A. Dathan, F. M. Morel, C. T. Supuran, G. De Simone, S. M. Monti
Structural And Inhibition Insights Into Carbonic Anhydrase Cdca1 From The Marine Diatom Thalassiosira Weissflogii.
Biochimie V. 94 1232 2012
PubMed-ID: 22381359  |  Reference-DOI: 10.1016/J.BIOCHI.2012.02.013

(-) Compounds

Molecule 1 - CADMIUM-SPECIFIC CARBONIC ANHYDRASE
    Chains: A, B
    EC Number: 4.2.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN (CDCA1-R3), UNP RESIDUES 407-616
    Gene: CDCA1
    Organism Common: MARINE DIATOM
    Organism Scientific: THALASSIOSIRA WEISSFLOGII
    Organism Taxid: 67004

 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, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CD2Ligand/IonCADMIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CD-1Ligand/IonCADMIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CD-1Ligand/IonCADMIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:473 , HIS A:525 , CYS A:535 , ACT A:800 , HOH A:1050BINDING SITE FOR RESIDUE CD A 700
2AC2SOFTWARECYS A:473 , VAL A:474 , GLY A:536 , PHE A:537 , THR A:627 , LEU A:631 , CD A:700 , HOH A:1050BINDING SITE FOR RESIDUE ACT A 800
3AC3SOFTWARECYS B:473 , HIS B:525 , CYS B:535 , ACT B:800 , HOH B:1046BINDING SITE FOR RESIDUE CD B 700
4AC4SOFTWARECYS B:473 , VAL B:474 , GLY B:536 , PHE B:537 , THR B:627 , LEU B:631 , CD B:700 , HOH B:1046 , HOH B:1146BINDING SITE FOR RESIDUE ACT B 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UK8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UK8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UK8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UK8)

(-) Exons   (0, 0)

(no "Exon" information available for 3UK8)

(-) 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:214
 aligned with Q50EL4_THAWE | Q50EL4 from UniProtKB/TrEMBL  Length:616

    Alignment length:276
                                   350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610      
         Q50EL4_THAWE   341 GSHTEKVVYINLLANKTLEPNENDQRFIVDGWAADKFGLDVPKFLIAAAATVEMLGGPKNAKIVVPSITPPQIVSALRGRGWKASIVKASTMSSELKRVDPQGILKCVDGRGSDNTQFGGPKMPGGIYAIAHNRGVTTLEGLKDITREVASKGHVPSVHGDHSSDMLGCGFFKLWLTGRFDDMGYPRPEFDADQGALAVRAAGGVIEMHHGSHEEKVVYINLVSGMTLEPNEHDQRFIVDGWAASKFGLDVVKFLVAAAATVEMLGGPKKAKIVIP 616
               SCOP domains d3u                                                              k8a_ A: Cadmium-specific carbonic anhydrase CdCA1                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...--------------------------------------------------------------...hhhhhhhhhhhh..eeeeee.hhhh...ee.....ee.....................hhhhhhhhh..hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhh..eeeee........eeee....ee.........eeeehhhhhhh..hhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3uk8 A  -3 GSH--------------------------------------------------------------MSITPPQIVSALRGRGWKASIVKASTMSSELKRVDPQGILKCVDGRGSDNTQFGGPKMPGGIYAIAHNRGVTTLEGLKDITREVASKGHVPSVHGDHSSDMLGCGFFKLWLTGRFDDMGYPRPEFDADQGALAVRAAGGVIEMHHGSHEEKVVYINLVSGMTLEPNEHDQRFIVDGWAASKFGLDVVKFLVAAAATVEMLGGPKKAKIVIP 642
                              |      -         -         -         -         -         -     ||436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636      
                             -1                                                              0|                                                                                                                                                                                                                 
                                                                                            433                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:209
 aligned with Q50EL4_THAWE | Q50EL4 from UniProtKB/TrEMBL  Length:616

    Alignment length:209
                                   417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607         
         Q50EL4_THAWE   408 ITPPQIVSALRGRGWKASIVKASTMSSELKRVDPQGILKCVDGRGSDNTQFGGPKMPGGIYAIAHNRGVTTLEGLKDITREVASKGHVPSVHGDHSSDMLGCGFFKLWLTGRFDDMGYPRPEFDADQGALAVRAAGGVIEMHHGSHEEKVVYINLVSGMTLEPNEHDQRFIVDGWAASKFGLDVVKFLVAAAATVEMLGGPKKAKIVIP 616
               SCOP domains d3uk8b_ B: Cadmium-specific carbonic anhydrase CdCA1                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeeee........ee.....ee.....................hhhhhhhhh..hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhh............hhhhhhhhhhhh..eeeee........eeee....ee.........eeeehhhhhhh..hhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uk8 B 434 ITPPQIVSALRGRGWKASIVKASTMSSELKRVDPQGILKCVDGRGSDNTQFGGPKMPGGIYAIAHNRGVTTLEGLKDITREVASKGHVPSVHGDHSSDMLGCGFFKLWLTGRFDDMGYPRPEFDADQGALAVRAAGGVIEMHHGSHEEKVVYINLVSGMTLEPNEHDQRFIVDGWAASKFGLDVVKFLVAAAATVEMLGGPKKAKIVIP 642
                                   443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633
   Legend:   → Mismatch (orange background)
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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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UK8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UK8)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q50EL4_THAWE | Q50EL4)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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UniProtKB/TrEMBL
        Q50EL4_THAWE | Q50EL4: 3bob 3boc 3boe 3boh 3boj

(-) Related Entries Specified in the PDB File

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