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(-) Description

Title :  CRYSTAL STRUCTURE OF F65A/Y131C CARBONIC ANHYDRASE V, COVALENTLY MODIFIED WITH 4-CHLOROMETHYLIMIDAZOLE
 
Authors :  K. M. Jude, S. K. Wright, C. Tu, D. N. Silverman, R. E. Viola, D. W. Christianson
Date :  16 Nov 01  (Deposition) - 06 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Proton Transfer, Engineered Residue, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Jude, S. K. Wright, C. Tu, D. N. Silverman, R. E. Viola, D. W. Christianson
Crystal Structure Of F65A/Y131C-Methylimidazole Carbonic Anhydrase V Reveals Architectural Features Of An Engineered Proton Shuttle.
Biochemistry V. 41 2485 2002
PubMed-ID: 11851394  |  Reference-DOI: 10.1021/BI015808Q
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - F65A/Y131C-MI CARBONIC ANHYDRASE V
    Chains: A, B
    EC Number: 4.2.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET31 T7
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CARBONIC ANHYDRASE VC
    Gene: MCA5C
    Mutation: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
14MZ5Ligand/Ion4-METHYLIMIDAZOLE
2ACY3Ligand/IonACETIC ACID
3K1Ligand/IonPOTASSIUM ION
4ZN2Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:171 , GLN A:173 , HOH A:449 , ASP B:171 , GLN B:173BINDING SITE FOR RESIDUE K A 305
02AC2SOFTWAREHIS A:94 , HIS A:96 , HIS A:119 , ACY A:299 , HOH A:871BINDING SITE FOR RESIDUE ZN A 280
03AC3SOFTWAREHIS B:94 , HIS B:96 , HIS B:119 , ACY B:300 , HOH B:872BINDING SITE FOR RESIDUE ZN B 281
04AC4SOFTWAREGLN A:92 , CYS A:131 , SER A:135 , HOH A:577BINDING SITE FOR RESIDUE 4MZ A 350
05AC5SOFTWARECYS A:183BINDING SITE FOR RESIDUE 4MZ A 351
06AC6SOFTWARECYS A:188 , ASP A:190BINDING SITE FOR RESIDUE 4MZ A 352
07AC7SOFTWARECYS B:183BINDING SITE FOR RESIDUE 4MZ B 351
08AC8SOFTWARECYS B:188 , ASP B:190BINDING SITE FOR RESIDUE 4MZ B 352
09AC9SOFTWAREHIS A:94 , HIS A:119 , LEU A:198 , THR A:199 , ZN A:280 , HOH A:871BINDING SITE FOR RESIDUE ACY A 299
10BC1SOFTWAREHIS B:94 , HIS B:119 , LEU B:198 , THR B:199 , TRP B:209 , ZN B:281 , HOH B:872BINDING SITE FOR RESIDUE ACY B 300
11BC2SOFTWARELEU A:47 , VAL A:49 , ARG A:189 , HOH A:498 , HOH A:558 , HOH A:696BINDING SITE FOR RESIDUE ACY A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:29 -Pro A:30
2Pro A:201 -Pro A:202
3Ser B:29 -Pro B:30
4Pro B:201 -Pro B:202

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHA_CA_1PS00162 Alpha-carbonic anhydrases signature.CAH5A_MOUSE135-151
 		  2A:105-121
B:105-121

(-) Exons   (0, 0)

(no "Exon" information available for 1KEQ)

(-) 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:238
 aligned with CAH5A_MOUSE | P23589 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:238
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284        
          CAH5A_MOUSE    55 GTRQSPINIQWKDSVYDPQLAPLRVSYDAASCRYLWNTGYFFQVEFDDSCEDSGISGGPLGNHYRLKQFHFHWGATDEWGSEHAVDGHTYPAELHLVHWNSTKYENYKKASVGENGLAVIGVFLKLGAHHQALQKLVDVLPEVRHKDTQVAMGPFDPSCLLPACRDYWTYPGSLTTPPLAESVTWIVQKTPVEVSPSQLSTFRTLLFSGRGEEEDVMVNNYRPLQPLRDRKLRSSFRL 292
               SCOP domains d1keqa_ A: Carbonic anhydrase                                                                                                                                                                                                                  SCOP domains
               CATH domains 1keqA00 A:25-262 Carbonic Anhydrase II                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eehhh.eee....eeeeee.hhh.eeeeee....eeeee.......eeeee.....eeeeeeeeee..........ee......eeeeeeeee.....hhhhhh.....eeeeeeeeee...hhhhhhhhhhhhhh.....eee....hhhhhh.....eeeeee..........eeeeee...eeehhhhhhhhh............................eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------ALPHA_CA_1       --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1keq A  25 GTRQSPINIQWKDSVYDPQLAPLRVSYDAASCRYLWNTGYAFQVEFDDSCEDSGISGGPLGNHYRLKQFHFHWGATDEWGSEHAVDGHTYPAELHLVHWNSTKYENCKKASVGENGLAVIGVFLKLGAHHQALQKLVDVLPEVRHKDTQVAMGPFDPSCLMPACRDYWTYPGSLTTPPLAESVTWIVQKTPVEVSPSQLSMFRTLLFSGRGEEEDVMVNNYRPLQPLRDRKLRSSFRL 262
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254        


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with CAH5A_MOUSE | P23589 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:238
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284        
          CAH5A_MOUSE    55 GTRQSPINIQWKDSVYDPQLAPLRVSYDAASCRYLWNTGYFFQVEFDDSCEDSGISGGPLGNHYRLKQFHFHWGATDEWGSEHAVDGHTYPAELHLVHWNSTKYENYKKASVGENGLAVIGVFLKLGAHHQALQKLVDVLPEVRHKDTQVAMGPFDPSCLLPACRDYWTYPGSLTTPPLAESVTWIVQKTPVEVSPSQLSTFRTLLFSGRGEEEDVMVNNYRPLQPLRDRKLRSSFRL 292
               SCOP domains d1keqb_ B: Carbonic anhydrase                                                                                                                                                                                                                  SCOP domains
               CATH domains 1keqB00 B:25-262 Carbonic Anhydrase II                                                                                                                                                                                                         CATH domains
           Pfam domains (1) Carb_anhydrase-1keqB01 B:25-260                                                                                                                                                                                                             -- Pfam domains (1)
           Pfam domains (2) Carb_anhydrase-1keqB02 B:25-260                                                                                                                                                                                                             -- Pfam domains (2)
         Sec.struct. author .......eehhh.eee....eeeeee.hhh.eeeeee....eeeee.......eeeee.....eeeeeeeeee..........ee......eeeeeeeee.....hhhhhh.....eeeeeeeeee...hhhhhhhhhhhhhhh....eee....hhhhhh.....eeeeee..........eeeeee...eeehhhhhhhhh............................eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------ALPHA_CA_1       --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1keq B  25 GTRQSPINIQWKDSVYDPQLAPLRVSYDAASCRYLWNTGYAFQVEFDDSCEDSGISGGPLGNHYRLKQFHFHWGATDEWGSEHAVDGHTYPAELHLVHWNSTKYENCKKASVGENGLAVIGVFLKLGAHHQALQKLVDVLPEVRHKDTQVAMGPFDPSCLMPACRDYWTYPGSLTTPPLAESVTWIVQKTPVEVSPSQLSMFRTLLFSGRGEEEDVMVNNYRPLQPLRDRKLRSSFRL 262
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Carb_anhydrase] (168)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CAH5A_MOUSE | P23589)
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:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
cellular component
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CAH5A_MOUSE | P23589: 1dmx 1dmy 1urt

(-) Related Entries Specified in the PDB File

1dmx WT CA-V