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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   N-TERMINAL DOMAIN OF TISSUE INHIBITOR OF METALLOPROTEINASE-2 (N-TIMP-2), NMR, 49 STRUCTURES

Authors :   F. W. Muskett, T. A. Frenkiel, J. Feeney, R. B. Freedman, M. D. Carr, R. A. Williamson

Date :   26 May 98 (Deposition) - 09 Dec 98 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (49x)

Keywords :   Timp, Metalloproteinase Inhibitor, Ob Protein Fold, Metalloprotease Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. W. Muskett, T. A. Frenkiel, J. Feeney, R. B. Freedman, M. D. Carr, R. A. Williamson
High Resolution Structure Of The N-Terminal Domain Of Tissue Inhibitor Of Metalloproteinases-2 And Characterization Of Its Interaction Site With Matrix Metalloproteinase-3.
J. Biol. Chem. V. 273 21736 1998
PubMed-ID: 9705310 | Reference-DOI: 10.1074/JBC.273.34.21736
(for further references see the PDB file header)

Molecule 1 - TISSUE INHIBITOR OF METALLOPROTEINASES-2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Cellular Location	:	INTRACELLULAR INCLUSION BODIES
	Expression System Plasmid	:	PET23D
	Expression System Strain	:	BL21
	Expression System Taxid	:	469008
	Expression System Variant	:	DE3
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN, RESIDUES 1-127
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	PROTEIN REFOLDED FROM INCLUSION BODIES
	Synonym	:	METALLOPROTEINASE INHIBITOR, TIMP-2


NMR Structure (49x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2TMP)

(no "Site" information available for 2TMP)

NMR Structure

No.	Residues
1	A:1	-	A:72
2	A:3	-	A:101
3	A:13	-	A:126

(no "Cis Peptide Bond" information available for 2TMP)

(no "SAP(SNP)/Variant" information available for 2TMP)

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NTR	PS50189	NTR domain profile.	TIMP2_HUMAN	27-152	1	A:1-126
2	TIMP	PS00288	Tissue inhibitors of metalloproteinases signature.	TIMP2_HUMAN	27-39	1	A:1-13

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000262768	1	ENSE00001319888	chr17:76921469-76921041	429	TIMP2_HUMAN	1-44	44	1	A:1-18	18
1.2b	ENST00000262768	2b	ENSE00001298704	chr17:76870001-76869901	101	TIMP2_HUMAN	44-77	34	1	A:18-51	34
1.3	ENST00000262768	3	ENSE00000745851	chr17:76867088-76866980	109	TIMP2_HUMAN	78-114	37	1	A:52-88	37
1.4a	ENST00000262768	4a	ENSE00001033832	chr17:76853728-76853604	125	TIMP2_HUMAN	114-155	42	1	A:88-127	40
1.5b	ENST00000262768	5b	ENSE00001317697	chr17:76851946-76849059	2888	TIMP2_HUMAN	156-220	65	0	-	-

NMR Structure

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
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Chain A from PDB  Type:PROTEIN  Length:127
 aligned with TIMP2_HUMAN | P16035 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:127
                                    36        46        56        66        76        86        96       106       116       126       136       146       
          TIMP2_HUMAN    27 CSCSPVHPQQAFCNADVVIRAKAVSEKEVDSGNDIYGNPIKRIQYEIKQIKMFKGPEKDIEFIYTAPSSAVCGVSLDVGGKKEYLIAGKAEGDGKMHITLCDFIVPWDTLSTTQKKSLNHRYQMGCE 153
               SCOP domains d2tmpa_ A: TIMP-2                                                                                                               SCOP domains
               CATH domains 2tmpA00 A:1-127  [code=2.40.50.120, no name defined]                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................................eee...............eee............................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) NTR  PDB: A:1-126 UniProt: 27-152                                                                                             - PROSITE (1)
                PROSITE (2) TIMP         ------------------------------------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.1          ---------------------------------Exon 1.3  PDB: A:52-88               --------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.2b  PDB: A:18-51           ------------------------------------Exon 1.4a  PDB: A:88-127 [INCOMPLETE]    Transcript 1 (2)
                 2tmp A   1 CSCSPVHPQQAFCNADVVIRTKAVSEKEVDSGNDIYGNPIKRIQYEIKQIKMFKGPEKDIEFIYTAPSSAVCGVSLDVGGKKEYLIAGKAEGDGKMHITLCDFIVPWDTLSTTQKKSLNHRYQMGCE 127
                                    10        20        30        40        50        60        70        80        90       100       110       120

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: OB-fold (1179)

Superfamily: TIMP-like (22)

Family: Tissue inhibitor of metalloproteinases, TIMP (13)

Protein domain: TIMP-2 (7)

Human (Homo sapiens) [TaxId: 9606] (4)

d2tmpa_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: [code=2.40.50.120, no name defined] (16)

Human (Homo sapiens) (12)

2tmpA00

A:1-127

(no "Pfam Domain" information available for 2TMP)

NMR Structure(hide GO term definitions)

Chain A (TIMP2_HUMAN | P16035)

molecular function
	GO:0004857	enzyme inhibitor activity	Binds to and stops, prevents or reduces the activity of an enzyme.
	GO:0005178	integrin binding	Interacting selectively and non-covalently with an integrin.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008191	metalloendopeptidase inhibitor activity	Stops, prevents or reduces the activity of metalloendopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain and contain a chelated metal ion at their active sites which is essential to their catalytic activity.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0002020	protease binding	Interacting selectively and non-covalently with any protease or peptidase.
	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).
biological process
	GO:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
	GO:0007417	central nervous system development	The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
	GO:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0046580	negative regulation of Ras protein signal transduction	Any process that stops, prevents, or reduces the frequency, rate or extent of Ras protein signal transduction.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0051045	negative regulation of membrane protein ectodomain proteolysis	Any process that stops, prevents, or reduces the frequency, rate or extent of membrane protein ectodomain proteolysis.
	GO:0045930	negative regulation of mitotic cell cycle	Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
	GO:0045861	negative regulation of proteolysis	Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
	GO:0043410	positive regulation of MAPK cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
	GO:0045762	positive regulation of adenylate cyclase activity	Any process that activates or increases the frequency, rate or extent of adenylate cyclase activity.
	GO:0045666	positive regulation of neuron differentiation	Any process that activates or increases the frequency, rate or extent of neuron differentiation.
	GO:0032487	regulation of Rap protein signal transduction	Any process that modulates the frequency, rate or extent of Rap protein signal transduction.
	GO:0034097	response to cytokine	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 cytokine stimulus.
	GO:0042493	response to drug	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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0009725	response to 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 hormone stimulus.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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:0030426	growth cone	The migrating motile tip of a growing nerve cell axon or dendrite.
	GO:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

NMR Structure
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	2tmp
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	TIMP2_HUMAN \| P16035	:	1br9 1gxd 4ilw

(no "Related Entries Specified in the PDB File" available for 2TMP)

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SS Bonds (3, 3)

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