3P4V - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   HUMAN CARBONIC ANHYDRASE II IN COMPLEX WITH (+)-XYLARIAMIDE A

Authors :   A. Hofmann, T. Nankervis, R. Davis

Date :   07 Oct 10 (Deposition) - 20 Apr 11 (Release) - 20 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Carbonic Anhydrase, Alpha Type, Lyase-Lyase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. A. Davis, A. Hofmann, A. Osman, R. A. Hall, F. A. Muhlschlegel, D. Vullo, A. Innocenti, C. T. Supuran, S. A. Poulsen
Natural Product-Based Phenols As Novel Probes For Mycobacterial And Fungal Carbonic Anhydrases.
J. Med. Chem. V. 54 1682 2011
PubMed-ID: 21332115 | Reference-DOI: 10.1021/JM1013242

Molecule 1 - CARBONIC ANHYDRASE 2
	Chains	:	A
	EC Number	:	4.2.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET8C
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CA2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CARBONIC ANHYDRASE II, CA-II, CARBONATE DEHYDRATASE II, CARBONIC ANHYDRASE C, CAC

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	PMX	1	Ligand/Ion	3-CHLORO-N-[(2E)-4-METHOXY-4-OXOBUT-2-ENOYL]-L-TYROSINE
2	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:94 , HIS A:96 , HIS A:119 , HOH A:267	BINDING SITE FOR RESIDUE ZN A 261
2	AC2	SOFTWARE	ASN A:67 , GLN A:92 , PHE A:130 , VAL A:134 , LEU A:197 , THR A:198 , PRO A:201 , LEU A:203 , TRP A:208 , HOH A:280 , HOH A:283 , HOH A:336 , HOH A:372 , HOH A:403	BINDING SITE FOR RESIDUE PMX A 300

(no "SS Bond" information available for 3P4V)

Asymmetric/Biological Unit

No.	Residues
1	Ser A:29	-	Pro A:30
2	Pro A:200	-	Pro A:201

Asymmetric/Biological Unit (7, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_001380	K	18	E	CAH2_HUMAN	Polymorphism	118203931	A	K	18	E
2	UniProt	VAR_001381	Q	92	P	CAH2_HUMAN	Disease (OPTB3)	---	A	Q	92	P
3	UniProt	VAR_021009	H	94	Y	CAH2_HUMAN	Disease (OPTB3)	---	A	H	94	Y
4	UniProt	VAR_001382	H	107	Y	CAH2_HUMAN	Disease (OPTB3)	118203933	A	H	107	Y
5	UniProt	VAR_021010	G	144	R	CAH2_HUMAN	Disease (OPTB3)	---	A	G	144	R
6	UniProt	VAR_001383	P	236	H	CAH2_HUMAN	Polymorphism	118203932	A	P	236	H
7	UniProt	VAR_001384	N	252	D	CAH2_HUMAN	Polymorphism	2228063	A	N	252	D

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALPHA_CA_1	PS00162	Alpha-carbonic anhydrases signature.	CAH2_HUMAN	105-121	1	A:105-121

Asymmetric/Biological Unit (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000285379	1a	ENSE00000980911	chr8:86376081-86376344	264	CAH2_HUMAN	1-12	12	1	A:4-12	9
1.2	ENST00000285379	2	ENSE00000795076	chr8:86377501-86377698	198	CAH2_HUMAN	12-78	67	1	A:12-78	67
1.4a	ENST00000285379	4a	ENSE00000698423	chr8:86385922-86386040	119	CAH2_HUMAN	78-117	40	1	A:78-117	40
1.5a	ENST00000285379	5a	ENSE00000698425	chr8:86386553-86386645	93	CAH2_HUMAN	118-148	31	1	A:118-148	31
1.6	ENST00000285379	6	ENSE00000698427	chr8:86388027-86388089	63	CAH2_HUMAN	149-169	21	1	A:149-169	21
1.7b	ENST00000285379	7b	ENSE00000698429	chr8:86389349-86389504	156	CAH2_HUMAN	170-221	52	1	A:170-221	52
1.8b	ENST00000285379	8b	ENSE00001195849	chr8:86392899-86393693	795	CAH2_HUMAN	222-260	39	1	A:222-260	39

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:257
 aligned with CAH2_HUMAN | P00918 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:257
                                    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       
           CAH2_HUMAN     4 HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK 260
               SCOP domains d3p4va_ A: Carbonic anhydrase                                                                                                                                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -Carb_anhydrase-3p4vA01 A:5-259                                                                                                                                                                                                                                 - Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh......ee.....ee......eeee.....eeeeee....eeeee.......eeee......eeeeeeeeee..........ee......eeeeeeeee.hhhhhhhhh.....eeeeeeeeee...hhhhhhhhhhhhhhh....eee....hhhhhh.....eeeeee..........eeeeee...eeehhhhhhhhh.............................ee... Sec.struct. author
                 SAPs(SNPs) --------------E-------------------------------------------------------------------------P-Y------------Y------------------------------------R-------------------------------------------------------------------------------------------H---------------D-------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------ALPHA_CA_1       ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a-----------------------------------------------------------------Exon 1.4a  PDB: A:78-117 UniProt: 78-117Exon 1.5a  PDB: A:118-148      Exon 1.6             Exon 1.7b  PDB: A:170-221 UniProt: 170-221          Exon 1.8b  PDB: A:222-260               Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.2  PDB: A:12-78 UniProt: 12-78                              -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3p4v A   4 HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK 260
                                    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

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: Carbonic anhydrase (525)

Superfamily: Carbonic anhydrase (525)

Family: Carbonic anhydrase (513)

Protein domain: Carbonic anhydrase (499)

Human (Homo sapiens), erythrocytes, isozyme II [TaxId: 9606] (458)

d3p4va_

(no "CATH Domain" information available for 3P4V)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Carb_anhydrase] (168)

Family: Carb_anhydrase (168)

Homo sapiens (Human) (157)

Carb_anhydrase-3p4vA01

A:5-259

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CAH2_HUMAN | P00918)

molecular function
	GO:0004064	arylesterase activity	Catalysis of the reaction: a phenyl acetate + H2O = a phenol + acetate.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0038166	angiotensin-activated signaling pathway	The series of molecular signals generated as a consequence of angiotensin II binding to an angiotensin receptor on the surface of the cell, and proceeding with the activated receptor transmitting the signal to a heterotrimeric G-protein complex to initiate a change in cell activity. Ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0015701	bicarbonate transport	The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0015670	carbon dioxide transport	The directed movement of carbon dioxide (CO2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0071498	cellular response to fluid shear stress	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fluid shear stress stimulus. Fluid shear stress is the force acting on an object in a system where the fluid is moving across a solid surface.
	GO:0001822	kidney development	The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
	GO:0002009	morphogenesis of an epithelium	The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.
	GO:0042475	odontogenesis of dentin-containing tooth	The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel.
	GO:0006730	one-carbon metabolic process	The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
	GO:0045780	positive regulation of bone resorption	Any process that activates or increases the frequency, rate or extent of bone resorption.
	GO:0032849	positive regulation of cellular pH reduction	Any process that activates or increases the frequency, rate, or extent of a process that reduces the internal pH of a cell.
	GO:2001150	positive regulation of dipeptide transmembrane transport	Any process that activates or increases the frequency, rate or extent of dipeptide transmembrane transport.
	GO:0045672	positive regulation of osteoclast differentiation	Any process that activates or increases the frequency, rate or extent of osteoclast differentiation.
	GO:0032230	positive regulation of synaptic transmission, GABAergic	Any process that activates, maintains or increases the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA).
	GO:0044070	regulation of anion transport	Any process that modulates the frequency, rate or extent of the directed movement of anions, atoms or small molecules with a net negative charge into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:2001225	regulation of chloride transport	Any process that modulates the frequency, rate or extent of chloride transport.
	GO:0051453	regulation of intracellular pH	Any process that modulates the internal pH of a cell, measured by the concentration of the hydrogen ion.
	GO:0043627	response to estrogen	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.
	GO:0010033	response to organic substance	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
	GO:0009268	response to pH	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus. pH is a measure of the acidity or basicity of an aqueous solution.
	GO:0048545	response to steroid hormone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus.
	GO:0010043	response to zinc ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a zinc ion stimulus.
	GO:0046903	secretion	The controlled release of a substance by a cell or a tissue.
cellular component
	GO:0045177	apical part of cell	The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	GO:0016323	basolateral plasma membrane	The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005902	microvillus	Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
	GO:0043209	myelin sheath	An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	3p4v
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(no "Related Entries Specified in the PDB File" available for 3P4V)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 7)

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Exons (7, 7)

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