2B3L - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF TYPE I HUMAN METHIONINE AMINOPEPTIDASE IN THE APO FORM

Authors :   A. Addlagatta, X. Hu, J. O. Liu, B. W. Matthews

Date :   20 Sep 05 (Deposition) - 22 Nov 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Methionine Aminopeptidase, Human, Hydrolase, Metalloprotease, Pitabread Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Addlagatta, X. Hu, J. O. Liu, B. W. Matthews
Structural Basis For The Functional Differences Between Typ I And Type Ii Human Methionine Aminopeptidases(, ).
Biochemistry V. 44 14741 2005
PubMed-ID: 16274222 | Reference-DOI: 10.1021/BI051691K

Molecule 1 - METHIONINE AMINOPEPTIDASE 1
	Chains	:	A
	EC Number	:	3.4.11.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 81-384
	Gene	:	METAP1, KIAA0094
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	METAP 1, MAP 1, PEPTIDASE M 1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL
3	K	1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:205 , ASN A:207 , VAL A:209 , SER A:363 , HOH A:665 , HOH A:768	BINDING SITE FOR RESIDUE K A 403
2	AC2	SOFTWARE	THR A:172 , THR A:204 , SER A:205 , VAL A:206 , VAL A:209 , ILE A:214 , ASP A:216 , ARG A:218 , HOH A:511 , HOH A:547	BINDING SITE FOR RESIDUE GOL A 470
3	AC3	SOFTWARE	HIS A:212 , CYS A:301 , HIS A:310 , GLU A:336 , HOH A:543 , HOH A:634 , HOH A:683 , HOH A:821 , HOH A:825 , HOH A:978	BINDING SITE FOR RESIDUE GOL A 471
4	AC4	SOFTWARE	PHE A:198 , CYS A:203 , HOH A:634 , HOH A:882	BINDING SITE FOR RESIDUE ACY A 472

(no "SS Bond" information available for 2B3L)

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:100	-	Pro A:101
2	Ala A:312	-	Pro A:313

(no "SAP(SNP)/Variant" information available for 2B3L)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MAP_1	PS00680	Methionine aminopeptidase subfamily 1 signature.	MAP11_HUMAN	291-309	1	A:300-318

Asymmetric/Biological Unit (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000296411	1a	ENSE00001131279	chr4:99916771-99917018	248	MAP11_HUMAN	1-38	38	0	-	-
1.5	ENST00000296411	5	ENSE00001080641	chr4:99950018-99950069	52	MAP11_HUMAN	39-56	18	0	-	-
1.7a	ENST00000296411	7a	ENSE00001080639	chr4:99955381-99955493	113	MAP11_HUMAN	56-93	38	1	A:89-102	14
1.8	ENST00000296411	8	ENSE00001080648	chr4:99956551-99956611	61	MAP11_HUMAN	94-114	21	1	A:103-123	21
1.12c	ENST00000296411	12c	ENSE00001080645	chr4:99960525-99960616	92	MAP11_HUMAN	114-144	31	1	A:123-153	31
1.13	ENST00000296411	13	ENSE00001080638	chr4:99962194-99962277	84	MAP11_HUMAN	145-172	28	1	A:154-181	28
1.14c	ENST00000296411	14c	ENSE00001080643	chr4:99964400-99964538	139	MAP11_HUMAN	173-219	47	1	A:182-228	47
1.15b	ENST00000296411	15b	ENSE00001080647	chr4:99966330-99966461	132	MAP11_HUMAN	219-263	45	1	A:228-272	45
1.16	ENST00000296411	16	ENSE00001080640	chr4:99969884-99970027	144	MAP11_HUMAN	263-311	49	1	A:272-320	49
1.17	ENST00000296411	17	ENSE00001080646	chr4:99978904-99978969	66	MAP11_HUMAN	311-333	23	1	A:320-342	23
1.18c	ENST00000296411	18c	ENSE00001212900	chr4:99982305-99983964	1660	MAP11_HUMAN	333-386	54	1	A:342-393	52

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:305
 aligned with MAP11_HUMAN | P53582 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:305
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379     
          MAP11_HUMAN    80 GYRYTGKLRPHYPLMPTRPVPSYIQRPDYADHPLGMSESEQALKGTSQIKLLSSEDIEGMRLVCRLAREVLDVAAGMIKPGVTTEEIDHAVHLACIARNCYPSPLNYYNFPKSCCTSVNEVICHGIPDRRPLQEGDIVNVDITLYRNGYHGDLNETFFVGEVDDGARKLVQTTYECLMQAIDAVKPGVRYRELGNIIQKHAQANGFSVVRSYCGHGIHKLFHTAPNVPHYAKNKAVGVMKSGHVFTIEPMICEGGWQDETWPDGWTAVTRDGKRSAQFEHTLLVTDTGCEILTRRLDSARPHFMS 384
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2b3lA00 A:89-393 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhh....hhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..ee...hhhhh....eeee..eee.............eeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..ee.....eee......eeeee................eeee..eee.....eee......eee.....eee..eeeee....eee.........hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MAP_1              --------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7a     --------------------Exon 1.12c  PDB: A:123-153     Exon 1.13  PDB: A:154-181   Exon 1.14c  PDB: A:182-228 UniProt: 173-219    -------------------------------------------Exon 1.16  PDB: A:272-320 UniProt: 263-311       ---------------------Exon 1.18c  PDB: A:342-393 UniProt: 333-386          Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.8             --------------------------------------------------------------------------------------------------------Exon 1.15b  PDB: A:228-272 UniProt: 219-263  -----------------------------------------------Exon 1.17              --------------------------------------------------- Transcript 1 (2)
                 2b3l A  89 PYRYTGKLRPHYPLMPTRPVPSYIQRPDYADHPLGMSESEQALKGTSQIKLLSSEDIEGMRLVCRLAREVLDVAAGMIKPGVTTEEIDHAVHLACIARNCYPSPLNYYNFPKSCCTSVNEVICHGIPDRRPLQEGDIVNVDITLYRNGYHGDLNETFFVGEVDDGARKLVQTTYECLMQAIDAVKPGVRYRELGNIIQKHAQANGFSVVRSYCGHGIHKLFHTAPNVPHYAKNKAVGVMKSGHVFTIEPMICEGGWQDETWPDGWTAVTRDGKRSAQFEHTLLVTDTGCEILTRRLDSARPHFMS 393
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388

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 '\|'

(no "SCOP Domain" information available for 2B3L)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Creatine Amidinohydrolase (114)

Homologous Superfamily: Creatinase/methionine aminopeptidase superfamily (114)

Human (Homo sapiens) (21)

2b3lA00

A:89-393

(no "Pfam Domain" information available for 2B3L)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MAP11_HUMAN | P53582)

molecular function
	GO:0004177	aminopeptidase activity	Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
	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:0070006	metalloaminopeptidase activity	Catalysis of the hydrolysis of N-terminal amino acid residues from 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:0008235	metalloexopeptidase activity	Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of 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: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.
biological process
	GO:0031365	N-terminal protein amino acid modification	The alteration of the N-terminal amino acid residue in a protein.
	GO:0018206	peptidyl-methionine modification	The modification of peptidyl-methionine.
	GO:0070527	platelet aggregation	The adhesion of one platelet to one or more other platelets via adhesion molecules.
	GO:0070084	protein initiator methionine removal	The protein modification process in which the translation-initiating methionine or formylmethionine residue is removed from a protein.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0022400	regulation of rhodopsin mediated signaling pathway	Any process that modulates the frequency, rate or extent of rhodopsin-mediated signaling.
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
cellular component
	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:0022626	cytosolic ribosome	A ribosome located in the cytosol.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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
		ACY	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		Ala A:312 - Pro A:313	[ RasMol ]
		Tyr A:100 - Pro A:101	[ RasMol ]

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)

Access by PDB/NDB ID
	2b3l
		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
	MAP11_HUMAN \| P53582
		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)
	3.4.11.18
		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

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
	MAP11_HUMAN \| P53582
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

2b3h	TRIMETALLO FORM
2b3k	HOLO FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (9, 9)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (17, 17)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File