1R54 - JenaLib

Asym./Biol. Unit

Asym./Biol. Unit - sites

collapse

expand

Asym./Biol. Unit (Jmol Viewer)

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

Description

Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN ADAM33

Authors :   P. Orth, P. Reicher, W. Wang, W. W. Prosise, T. Yarosh-Tomaine, G. Hammo L. Xiao, U. A. Mirza, J. Zou, C. Strickland, S. S. Taremi

Date :   09 Oct 03 (Deposition) - 12 Oct 04 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym./Biol. Unit : A

Keywords :   Metalloprotease, Asthma, Adam, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Orth, P. Reichert, W. Wang, W. W. Prosise, T. Yarosh-Tomaine, G. Hammond, L. Xiao, U. A. Mirza, J. Zou, C. Strickland, S. S. Taremi, H. V. Le, V. Madison
Crystal Structre Of The Catalytic Domain Of Human Adam33
J. Mol. Biol. V. 335 129 2004
PubMed-ID: 14659745 | Reference-DOI: 10.1016/J.JMB.2003.10.037

Compounds

Molecule 1 - ADAM 33
	Chains	:	A
	EC Number	:	3.4.24.-
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Common	:	FRUIT FLY
	Expression System Plasmid	:	PMT/BIP/V5-HISC
	Expression System Strain	:	S2
	Expression System Taxid	:	7227
	Expression System Vector Type	:	EUKARYOTIC VECTOR
	Fragment	:	RESIDUES 204-409
	Gene	:	ADAM33
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	A DISINTEGRIN AND METALLOPROTEINASE DOMAIN 33

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 6)

Asymmetric/Biological Unit (4, 6)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	CL	2	Ligand/Ion	CHLORIDE ION
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	ZN	1	Ligand/Ion	ZINC ION

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:276 , TRP A:280 , NAG A:511	BINDING SITE FOR RESIDUE NAG A 510
2	AC2	SOFTWARE	ARG A:293 , NAG A:510	BINDING SITE FOR RESIDUE NAG A 511
3	AC3	SOFTWARE	HOH A:23 , GLU A:204 , HIS A:345 , HIS A:349 , HIS A:355	BINDING SITE FOR RESIDUE ZN A 201
4	AC4	SOFTWARE	HOH A:4 , HOH A:10 , GLU A:213 , ASP A:296 , CYS A:404 , ASN A:407	BINDING SITE FOR RESIDUE CA A 202
5	AC5	SOFTWARE	HOH A:9 , HOH A:88 , SER A:333 , ARG A:398	BINDING SITE FOR RESIDUE CL A 203
6	AC6	SOFTWARE	HOH A:18 , ARG A:226 , ARG A:236 , ARG A:398	BINDING SITE FOR RESIDUE CL A 512

SS Bonds (3, 3)

Asymmetric/Biological Unit

No.	Residues
1	A:320	-	A:404
2	A:360	-	A:388
3	A:361	-	A:371

Cis Peptide Bonds (1, 1)

Asymmetric/Biological Unit

No.	Residues
1	His A:379	-	Pro A:380

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 5)

Asymmetric/Biological Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_030513	T	272	M	ADA33_HUMAN	Polymorphism	41534847	A	T	272	M
2	UniProt	VAR_066337	A	305	V	ADA33_HUMAN	Unclassified	---	A	A	305	V
3	UniProt	VAR_030514	V	316	I	ADA33_HUMAN	Polymorphism	41459049	A	V	316	I
4	UniProt	VAR_030515	P	336	S	ADA33_HUMAN	Polymorphism	41483049	A	P	336	S
5	UniProt	VAR_030516	A	365	S	ADA33_HUMAN	Polymorphism	41419248	A	A	365	S

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

PROSITE Motifs (2, 2)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADAM_MEPRO	PS50215	ADAM type metalloprotease domain profile.	ADA33_HUMAN	210-409	1	A:210-409
2	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	ADA33_HUMAN	342-351	1	A:342-351

Exons (6, 6)

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000356518	1a	ENSE00001943353	chr20:3662893-3662555	339	ADA33_HUMAN	1-33	33	0	-	-
1.2	ENST00000356518	2	ENSE00001162726	chr20:3660218-3660139	80	ADA33_HUMAN	33-59	27	0	-	-
1.3	ENST00000356518	3	ENSE00001162723	chr20:3657790-3657714	77	ADA33_HUMAN	60-85	26	0	-	-
1.4a	ENST00000356518	4a	ENSE00001386761	chr20:3655752-3655674	79	ADA33_HUMAN	85-111	27	0	-	-
1.5	ENST00000356518	5	ENSE00000990640	chr20:3655496-3655420	77	ADA33_HUMAN	112-137	26	0	-	-
1.6	ENST00000356518	6	ENSE00000990641	chr20:3655340-3655151	190	ADA33_HUMAN	137-200	64	0	-	-
1.7	ENST00000356518	7	ENSE00001655537	chr20:3654931-3654866	66	ADA33_HUMAN	201-222	22	1	A:204-222	19
1.8	ENST00000356518	8	ENSE00001787461	chr20:3654782-3654711	72	ADA33_HUMAN	223-246	24	1	A:223-246	24
1.9b	ENST00000356518	9b	ENSE00001766750	chr20:3654558-3654392	167	ADA33_HUMAN	247-302	56	1	A:247-302	56
1.9e	ENST00000356518	9e	ENSE00001709035	chr20:3654305-3654221	85	ADA33_HUMAN	302-330	29	1	A:302-330	29
1.10a	ENST00000356518	10a	ENSE00001614585	chr20:3654143-3654001	143	ADA33_HUMAN	331-378	48	1	A:331-378	48
1.10e	ENST00000356518	10e	ENSE00001598605	chr20:3653545-3653368	178	ADA33_HUMAN	378-437	60	1	A:378-409	32
1.11	ENST00000356518	11	ENSE00002159586	chr20:3653273-3653184	90	ADA33_HUMAN	438-467	30	0	-	-
1.12	ENST00000356518	12	ENSE00001601961	chr20:3652976-3652781	196	ADA33_HUMAN	468-533	66	0	-	-
1.13a	ENST00000356518	13a	ENSE00001640837	chr20:3652632-3652524	109	ADA33_HUMAN	533-569	37	0	-	-
1.14	ENST00000356518	14	ENSE00002191279	chr20:3652426-3652228	199	ADA33_HUMAN	569-635	67	0	-	-
1.15	ENST00000356518	15	ENSE00001786400	chr20:3652143-3652066	78	ADA33_HUMAN	636-661	26	0	-	-
1.16	ENST00000356518	16	ENSE00001622157	chr20:3651992-3651884	109	ADA33_HUMAN	662-698	37	0	-	-
1.17a	ENST00000356518	17a	ENSE00001664552	chr20:3651800-3651653	148	ADA33_HUMAN	698-747	50	0	-	-
1.18c	ENST00000356518	18c	ENSE00001698260	chr20:3650284-3650193	92	ADA33_HUMAN	747-778	32	0	-	-
1.18d	ENST00000356518	18d	ENSE00001641345	chr20:3650017-3649946	72	ADA33_HUMAN	778-802	25	0	-	-
1.19b	ENST00000356518	19b	ENSE00001936716	chr20:3649647-3648617	1031	ADA33_HUMAN	802-813	12	0	-	-

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:206
 aligned with ADA33_HUMAN | Q9BZ11 from UniProtKB/Swiss-Prot  Length:813

    Alignment length:206
                                   213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403      
          ADA33_HUMAN   204 EARRTRKYLELYIVADHTLFLTRHRNLNHTKQRLLEVANYVDQLLRTLDIQVALTGLEVWTERDRSRVTQDANATLWAFLQWRRGLWAQRPHDSAQLLTGRAFQGATVGLAPVEGMCRAESSGGVSTDHSELPIGAAATMAHEIGHSLGLSHDPDGCCVEAAAESGGCVMAAATGHPFPRVFSACSRRQLRAFFRKGGGACLSNAP 409
               SCOP domains d1r54a_ A: ADAM33                                                                                                                                                                                              SCOP domains
               CATH domains 1r54A00 A:204-409 Collagenase (Catalytic Domain)                                                                                                                                                               CATH domains
               Pfam domains ------Reprolysin-1r54A01 A:210-409                                                                                                                                                                             Pfam domains
         Sec.struct. author ......eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhh...eeeeee.........ee............eeeee....hhhhhhhhhhhhhhhhh.............hhhhh................hhhhhhhhhhhhhh..hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------M--------------------------------V----------I-------------------S----------------------------S-------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------ADAM_MEPRO  PDB: A:210-409 UniProt: 210-409                                                                                                                                                              PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.7           Exon 1.8  PDB: A:223-246Exon 1.9b  PDB: A:247-302 UniProt: 247-302              ----------------------------Exon 1.10a  PDB: A:331-378 UniProt: 331-378     ------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------Exon 1.9e  PDB: A:302-330    -----------------------------------------------Exon 1.10e  PDB: A:378-409       Transcript 1 (2)
                 1r54 A 204 EARRTRKYLELYIVADHTLFLTRHRNLQHTKQRLLEVANYVDQLLRTLDIQVALTGLEVWTERDRSRVTQDANATLWAFLQWRRGLWAQRPHDSAQLLTGRAFQGATVGLAPVEGMCRAESSGGVSTDHSELPIGAAATMAHEIGHSLGLSHDPDGCCVEAAAESGGCVMAAATGHPFPRVFSACSRRQLRAFFRKGGGACLSNAP 409
                                   213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Zincin-like (701)

Superfamily: Metalloproteases (zincins), catalytic domain (647)

Family: Reprolysin-like (24)

Protein domain: ADAM33 (2)

Human (Homo sapiens) [TaxId: 9606] (2)

d1r54a_

CATH Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Collagenase (Catalytic Domain) (236)

Homologous Superfamily: Collagenase (Catalytic Domain) (234)

Human (Homo sapiens) (153)

1r54A00

A:204-409

Pfam Domains (1, 1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_MA (251)

Family: Reprolysin (9)

Homo sapiens (Human) (9)

Reprolysin-1r54A01

A:210-409

Gene Ontology (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ADA33_HUMAN | Q9BZ11)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		His A:379 - Pro A:380	[ RasMol ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1r54
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ADA33_HUMAN \| Q9BZ11
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.4.24.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	ADA33_HUMAN \| Q9BZ11
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	ADA33_HUMAN \| Q9BZ11	:	1r55

Related Entries Specified in the PDB File

1r55	CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN ADAM 33