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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURES OF YRDA FROM ESCHERICHIA COLI, A HOMOLOGOUS PROTEIN OF GAMMA-CLASS CARBONIC ANHYDRASES, SHOW POSSIBLE ALLOSTERIC CONFORMATIONS

Authors :   H. M. Park, J. W. Chio, J. E. Lee, J. H. Jung, B. Y. Kim, J. S. Kim

Date :   21 Aug 11 (Deposition) - 01 Aug 12 (Release) - 29 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Carbonic Anhydrase (Ca), Zn Biding, Phosphate Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. M. Park, J. H. Park, J. W. Choi, J. E. Lee, B. Y. Kim, C. H. Jung, J. S. Kim
Structures Of The Gamma-Class Carbonic Anhydrase Homologue Yrda Suggest A Possible Allosteric Switch
Acta Crystallogr. , Sect. D V. 68 920 2012
PubMed-ID: 22868757 | Reference-DOI: 10.1107/S0907444912017210

Molecule 1 - PROTEIN YRDA
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YRDA, B3279, JW5710
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

No.	Name	Count	Type	Full Name
1	ZN	3	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:67 , HIS A:70 , HIS A:96 , HIS C:91	BINDING SITE FOR RESIDUE ZN A 185
2	AC2	SOFTWARE	HIS A:91 , HOH A:244 , HIS B:67 , VAL B:68 , HIS B:96	BINDING SITE FOR RESIDUE ZN B 185
3	AC3	SOFTWARE	HIS B:91 , HIS C:67 , HIS C:70 , HIS C:96	BINDING SITE FOR RESIDUE ZN C 1

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

Asymmetric/Biological Unit

No.	Residues
1	Ser A:145	-	Pro A:146
2	Ser B:145	-	Pro B:146
3	Ser C:145	-	Pro C:146

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

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

(no "Exon" information available for 3TIS)

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:174
 aligned with YRDA_ECOLI | P0A9W9 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171         
           YRDA_ECOLI     2 SDVLRPYRDLFPQIGQRVMIDDSSVVIGDVRLADDVGIWPLVVIRGDVHYVQIGARTNIQDGSMLHVTHKSSYNPDGNPLTIGEDVTVGHKVMLHGCTIGNRVLVGMGSILLDGAIVEDDVMIGAGSLVPQNKRLESGYLYLGSPVKQIRPLSDEEKAGLRYSANNYVKWKDEYLDQGN 180
               SCOP domains d3tisa_ A: automated matches                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......ee....ee....eeeeeeee....ee....eeeeeeeeeee....ee....eee.....-----...eee....ee....eee..ee...eee....ee....ee...eee....ee....ee...eeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tis A   2 SDVLHPYRDLFPQIGQRVMIDDSSVVIGDVRLADDVGIWPLVVIRGDVHYVQIGARTNIQDGSMLHVTHKS-----GNPLTIGEDVTVGHKVMLHGCTIGNRVLVGMGSILLDGAIVEDDVMIGAGSLVPQNKRLESGYLYLGSPVKQIRPLSDEEKAGLRYSANNYVKWKDEYLDQGN 180
                                    11        21        31        41        51        61        71|     | 81        91       101       111       121       131       141       151       161       171         
                                                                                                 72    78

Chain B from PDB  Type:PROTEIN  Length:176
 aligned with YRDA_ECOLI | P0A9W9 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:176
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172      
           YRDA_ECOLI     3 DVLRPYRDLFPQIGQRVMIDDSSVVIGDVRLADDVGIWPLVVIRGDVHYVQIGARTNIQDGSMLHVTHKSSYNPDGNPLTIGEDVTVGHKVMLHGCTIGNRVLVGMGSILLDGAIVEDDVMIGAGSLVPQNKRLESGYLYLGSPVKQIRPLSDEEKAGLRYSANNYVKWKDEYLDQ 178
               SCOP domains d3tisb_ B: automated matches                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.......ee....ee....eeeeeeee....ee....eeeeeeeeeee....ee....eee.............eee....ee....eee..ee...eee....ee....ee...eee....ee....ee...eeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tis B   3 DVLHPYRDLFPQIGQRVMIDDSSVVIGDVRLADDVGIWPLVVIRGDVHYVQIGARTNIQDGSMLHVTHKSSYNPDGNPLTIGEDVTVGHKVMLHGCTIGNRVLVGMGSILLDGAIVEDDVMIGAGSLVPQNKRLESGYLYLGSPVKQIRPLSDEEKAGLRYSANNYVKWKDEYLDQ 178
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain C from PDB  Type:PROTEIN  Length:170
 aligned with YRDA_ECOLI | P0A9W9 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:176
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172      
           YRDA_ECOLI     3 DVLRPYRDLFPQIGQRVMIDDSSVVIGDVRLADDVGIWPLVVIRGDVHYVQIGARTNIQDGSMLHVTHKSSYNPDGNPLTIGEDVTVGHKVMLHGCTIGNRVLVGMGSILLDGAIVEDDVMIGAGSLVPQNKRLESGYLYLGSPVKQIRPLSDEEKAGLRYSANNYVKWKDEYLDQ 178
               SCOP domains d3tisc_ C: automated matches                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.......ee....ee....eeeeeeee....ee....eeeeeeeeeee....ee....eee....------...eee....ee....eee..ee...eee....ee....ee...eee....ee....ee...eeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tis C   3 DVLHPYRDLFPQIGQRVMIDDSSVVIGDVRLADDVGIWPLVVIRGDVHYVQIGARTNIQDGSMLHVTHK------GNPLTIGEDVTVGHKVMLHGCTIGNRVLVGMGSILLDGAIVEDDVMIGAGSLVPQNKRLESGYLYLGSPVKQIRPLSDEEKAGLRYSANNYVKWKDEYLDQ 178
                                    12        22        32        42        52        62        |-     |  82        92       102       112       122       132       142       152       162       172      
                                                                                               71     78

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Single-stranded left-handed beta-helix (154)

Superfamily: Trimeric LpxA-like enzymes (147)

Family: automated matches (55)

Protein domain: automated matches (55)

Escherichia coli K-12 [TaxId: 83333] (2)

1a	d3tisa_	A:
1b	d3tisb_	B:
1c	d3tisc_	C:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (YRDA_ECOLI | P0A9W9)

molecular function
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ser A:145 - Pro A:146	[ RasMol ]
		Ser B:145 - Pro B:146	[ RasMol ]
		Ser C:145 - Pro C:146	[ RasMol ]

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	3tis
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	YRDA_ECOLI \| P0A9W9
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		Interatomic Contacts of Structural Units	:	CSU
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	YRDA_ECOLI \| P0A9W9	:	3tio

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

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