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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN CARBONIC ANHYDRASE XII

Authors :   D. A. Whittington, A. Waheed, B. Ulmasov, G. N. Shah, J. H. Grubb, W. S. Sl D. W. Christianson

Date :   11 Jun 01 (Deposition) - 17 Aug 01 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Extracellular Domain, Human Carbonic Anhydrase Xii, Bitopic Membrane Protein, Type I Membrane Protein, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. A. Whittington, A. Waheed, B. Ulmasov, G. N. Shah, J. H. Grubb, W. S. Sly, D. W. Christianson
Crystal Structure Of The Dimeric Extracellular Domain Of Human Carbonic Anhydrase Xii, A Bitopic Membrane Protein Overexpressed In Certain Cancer Tumor Cells.
Proc. Natl. Acad. Sci. Usa V. 98 9545 2001
PubMed-ID: 11493685 | Reference-DOI: 10.1073/PNAS.161301298

Molecule 1 - CARBONIC ANHYDRASE XII
	Chains	:	A, B
	EC Number	:	4.2.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-11D
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	EXTRACELLULAR DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CARBONATE DEHYDRATASE XII, CA-XII, TUMOR ANTIGEN HOM-RCC- 3.1.3

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:94 , HIS A:96 , HIS A:119 , ACY A:801 , HOH A:1096	BINDING SITE FOR RESIDUE ZN A 901
2	AC2	SOFTWARE	HIS B:94 , HIS B:96 , HIS B:119 , ACY B:802 , HOH B:1071	BINDING SITE FOR RESIDUE ZN B 902
3	AC3	SOFTWARE	HIS A:94 , HIS A:119 , VAL A:143 , LEU A:198 , THR A:199 , ZN A:901 , HOH A:1057 , HOH A:1096	BINDING SITE FOR RESIDUE ACY A 801
4	AC4	SOFTWARE	HIS B:94 , HIS B:119 , VAL B:143 , LEU B:198 , THR B:199 , ZN B:902 , HOH B:1071 , HOH B:1079	BINDING SITE FOR RESIDUE ACY B 802

Asymmetric/Biological Unit

No.	Residues
1	A:23	-	A:203
2	B:23	-	B:203

Asymmetric/Biological Unit

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

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_065292	E	143	K	CAH12_HUMAN	Disease (HCHLH)	267606694	A/B	E	117	K

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALPHA_CA_1	PS00162	Alpha-carbonic anhydrases signature.	CAH12_HUMAN	131-147	2	A:105-121 B:105-121

Asymmetric/Biological Unit (7, 14)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000178638	1a	ENSE00001916299	chr15:63674360-63673835	526	CAH12_HUMAN	1-29	29	0	-	-
1.2	ENST00000178638	2	ENSE00001033986	chr15:63667877-63667857	21	CAH12_HUMAN	29-36	8	2	A:4-9 B:4-9	6 6
1.3	ENST00000178638	3	ENSE00000931536	chr15:63638908-63638729	180	CAH12_HUMAN	36-96	61	2	A:9-66 B:9-66	61 61
1.4	ENST00000178638	4	ENSE00000931537	chr15:63637818-63637676	143	CAH12_HUMAN	96-143	48	2	A:66-117 (gaps) B:66-117 (gaps)	53 53
1.5	ENST00000178638	5	ENSE00000692813	chr15:63634296-63634201	96	CAH12_HUMAN	144-175	32	2	A:118-149 B:118-149	32 32
1.6	ENST00000178638	6	ENSE00000449602	chr15:63632982-63632919	64	CAH12_HUMAN	176-197	22	2	A:150-171 B:150-171	22 22
1.7	ENST00000178638	7	ENSE00000449603	chr15:63632644-63632487	158	CAH12_HUMAN	197-249	53	2	A:171-222 B:171-222	53 53
1.8	ENST00000178638	8	ENSE00001106427	chr15:63631144-63631018	127	CAH12_HUMAN	250-292	43	2	A:223-261 B:223-261	41 41
1.9	ENST00000178638	9	ENSE00000692799	chr15:63620329-63620297	33	CAH12_HUMAN	292-303	12	0	-	-
1.10	ENST00000178638	10	ENSE00000692794	chr15:63619432-63619348	85	CAH12_HUMAN	303-331	29	0	-	-
1.11c	ENST00000178638	11c	ENSE00001820066	chr15:63618556-63613577	4980	CAH12_HUMAN	331-354	24	0	-	-

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:260
 aligned with CAH12_HUMAN | O43570 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:260
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
         CAH12_HUMAN     31 KWTYFGPDGENSWSKKYPSCGGLLQSPIDLHSDILQYDASLTPLEFQGYNLSANKQFLLTNNGHSVKLNLPSDMHIQGLQSRYSATQLHLHWGNPNDPHGSEHTVSGQHFAAELHIVHYNSDLYPDASTASNKSEGLAVLAVLIEMGSFNPSYDKIFSHLQHVKYKGQEAFVPGFNIEELLPERTAEYYRYRGSLTTPPCNPTVLWTVFRNPVQISQEQLLALETALYCTHMDDPSPREMINNFRQVQKFDERLVYTSFS  290
               SCOP domains d1jcza_ A: Carbonic anhydrase                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1jczA00 A:4-261 Carbonic Anhydrase II                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh......eehhh.eee..................eeeeee....eeee.............eeeeeeeeee...........ee......eeeeeeeee.....hhhhhh.....eeeeeeeeee......hhhhhhhhhhh.....eeeee...hhhhh......eeeeee..........eeeeee...eeehhhhhhhhhhh............................eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------K--------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------ALPHA_CA_1       ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.2   -----------------------------------------------------------Exon 1.4  PDB: A:66-117 (gaps) UniProt: 96-143  Exon 1.5  PDB: A:118-149        Exon 1.6              ----------------------------------------------------Exon 1.8  PDB: A:223-261 UniProt: 250-292 Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.3  PDB: A:9-66 UniProt: 36-96                         ----------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:171-222 UniProt: 197-249            ----------------------------------------- Transcript 1 (2)
                1jcz A    4 KWTYFGPDGENSWSKKYPSCGGLLQSPIDLHSDILQYDASLTPLEFQGYNLSANKQFLLTNNGHSVKLNLPSDMHIQGLQSRYSATQLHLHWGNPNDPHGSEHTVSGQHFAAELHIVHYNSDLYPDASTASNKSEGLAVLAVLIEMGSFNPSYDKIFSHLQHVKYKGQEAFVPGFNIEELLPERTAEYYRYRGSLTTPPCNPTVLWTVFRNPVQISQEQLLALETALYCTHMDDPSPREMINNFRQVQKFDERLVYTSFS  261
                                    13        23        33        43       |52  ||    60        70   ||  |85        95       104       114       124       134       144       154       164       174       184   |   193       203       213       223       233       241       251       261
                                                                         50A  54A|                  74| 81|               102A                                                                                  187A                                                  240A|                     
                                                                               54B                   78  84                                                                                                                                                            240B

Chain B from PDB  Type:PROTEIN  Length:260
 aligned with CAH12_HUMAN | O43570 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:260
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
         CAH12_HUMAN     31 KWTYFGPDGENSWSKKYPSCGGLLQSPIDLHSDILQYDASLTPLEFQGYNLSANKQFLLTNNGHSVKLNLPSDMHIQGLQSRYSATQLHLHWGNPNDPHGSEHTVSGQHFAAELHIVHYNSDLYPDASTASNKSEGLAVLAVLIEMGSFNPSYDKIFSHLQHVKYKGQEAFVPGFNIEELLPERTAEYYRYRGSLTTPPCNPTVLWTVFRNPVQISQEQLLALETALYCTHMDDPSPREMINNFRQVQKFDERLVYTSFS  290
               SCOP domains d1jczb_ B: Carbonic anhydrase                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1jczB00 B:4-261 Carbonic Anhydrase II                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) -Carb_anhydrase-1jczB01 B:5-260                                                                                                                                                                                                                                    - Pfam domains (1)
           Pfam domains (2) -Carb_anhydrase-1jczB02 B:5-260                                                                                                                                                                                                                                    - Pfam domains (2)
         Sec.struct. author ........hhhhhhhhhhhhhh......eehhh.eee..................eeeeee....eeee.............eeeeeeeeee...........ee......eeeeeeeee.....hhhhhh.....eeeeeeeeee...hhhhhhhhhhhhhhh....eeeee...hhhhh......eeeeee..........eeeeee...eeehhhhhhhhhhhh...........................eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------K--------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------ALPHA_CA_1       ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.2   -----------------------------------------------------------Exon 1.4  PDB: B:66-117 (gaps) UniProt: 96-143  Exon 1.5  PDB: B:118-149        Exon 1.6              ----------------------------------------------------Exon 1.8  PDB: B:223-261 UniProt: 250-292 Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.3  PDB: B:9-66 UniProt: 36-96                         ----------------------------------------------------------------------------------------------------Exon 1.7  PDB: B:171-222 UniProt: 197-249            ----------------------------------------- Transcript 1 (2)
                1jcz B    4 KWTYFGPDGENSWSKKYPSCGGLLQSPIDLHSDILQYDASLTPLEFQGYNLSANKQFLLTNNGHSVKLNLPSDMHIQGLQSRYSATQLHLHWGNPNDPHGSEHTVSGQHFAAELHIVHYNSDLYPDASTASNKSEGLAVLAVLIEMGSFNPSYDKIFSHLQHVKYKGQEAFVPGFNIEELLPERTAEYYRYRGSLTTPPCNPTVLWTVFRNPVQISQEQLLALETALYCTHMDDPSPREMINNFRQVQKFDERLVYTSFS  261
                                    13        23        33        43       |52  ||    60        70   ||  |85        95       104       114       124       134       144       154       164       174       184   |   193       203       213       223       233       241       251       261
                                                                         50A  54A|                  74| 81|               102A                                                                                  187A                                                  240A|                     
                                                                               54B                   78  84                                                                                                                                                            240B

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), isozyme XII [TaxId: 9606] (5)

1a	d1jcza_	A:
1b	d1jczb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Carbonic Anhydrase II (332)

Homologous Superfamily: Carbonic Anhydrase II (332)

Human (Homo sapiens) (309)

1a	1jczA00	A:4-261
1b	1jczB00	B:4-261

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Carb_anhydrase (168)

Homo sapiens (Human) (157)

1a	Carb_anhydrase-1jczB01	B:5-260
1b	Carb_anhydrase-1jczB02	B:5-260

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CAH12_HUMAN | O43570)

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: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:0055064	chloride ion homeostasis	Any process involved in the maintenance of an internal steady state of chloride ions within an organism or cell.
	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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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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	CAH12_HUMAN \| O43570	:	1jd0 4ht2 4kp5 4kp8 4q0l 4qj0 4qjo 4qjw 4ww8

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Description

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Ligands, Modified Residues, Ions (2, 4)

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SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

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