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(-) Description

Title :  HUMAN METHIONINE AMINOPEPTIDASE-2 COMPLEXED WITH SB-587094
 
Authors :  J. P. Marino Jr. , P. W. Fisher, G. A. Hofmann, R. Kirkpatrick, C. A. Janson, R. K. Johnson, C. Ma, M. Mattern, T. D. Meek, D. Ryan, C. Schulz, W. W. Smith, D. G. Tew, T. A. Tomazek Jr. , D. F. Veber, W. C. Xiong, Y. Yamamoto, K. Yamashita, G. Yang, S. K. Thompson
Date :  18 Dec 06  (Deposition) - 19 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Metap2, Methionine, Amino Peptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Marino, P. W. Fisher, G. A. Hofmann, R. B. Kirkpatrick, C. A. Janson, R. K. Johnson, C. Ma, M. Mattern, T. D. Meek, M. D. Ryan, C. Schulz, W. W. Smith, D. G. Tew, T. A. Tomazek, D. F. Veber, W. C. Xiong, Y. Yamamoto, K. Yamashita, G. Yang, S. K. Thompson
Highly Potent Inhibitors Of Methionine Aminopeptidase-2 Based On A 1, 2, 4-Triazole Pharmacophore.
J. Med. Chem. V. 50 3777 2007
PubMed-ID: 17636946  |  Reference-DOI: 10.1021/JM061182W
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HUMAN METHIONINE AMINO PEPTIDASE 2
    Chains: A
    EC Number: 3.4.11.18
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CO2Ligand/IonCOBALT (II) ION
2I961Ligand/IonN-(2-ISOPROPYLPHENYL)-3-[(2-THIENYLMETHYL)THIO]-1H-1,2,4-TRIAZOL-5-AMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:251 , ASP A:262 , GLU A:459 , CO A:480 , I96 A:501BINDING SITE FOR RESIDUE CO A 479
2AC2SOFTWAREASP A:262 , HIS A:331 , GLU A:364 , GLU A:459 , CO A:479 , I96 A:501BINDING SITE FOR RESIDUE CO A 480
3AC3SOFTWAREPHE A:219 , HIS A:231 , ASP A:251 , ASP A:262 , ASN A:329 , GLU A:364 , HIS A:382 , TYR A:444 , LEU A:447 , CO A:479 , CO A:480BINDING SITE FOR RESIDUE I96 A 501

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:228 -A:448

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MAP_2PS01202 Methionine aminopeptidase subfamily 2 signature.MAP2_HUMAN246-262  1A:246-262

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003236661ENSE00001323969chr12:95867822-95868106285MAP2_HUMAN1-51510--
1.2aENST000003236662aENSE00000753403chr12:95869847-95869954108MAP2_HUMAN51-87370--
1.3ENST000003236663ENSE00000753404chr12:95876991-9587705666MAP2_HUMAN87-109230--
1.4ENST000003236664ENSE00000753405chr12:95879655-95879757103MAP2_HUMAN109-143351A:1-2929
1.5ENST000003236665ENSE00000753406chr12:95887832-95887993162MAP2_HUMAN143-197551A:153-19745
1.6ENST000003236666ENSE00000753407chr12:95888733-95888914182MAP2_HUMAN197-258621A:197-25862
1.7ENST000003236667ENSE00000753408chr12:95889780-9588987495MAP2_HUMAN258-289321A:258-28932
1.8ENST000003236668ENSE00000922696chr12:95897841-9589793797MAP2_HUMAN290-322331A:290-32233
1.9ENST000003236669ENSE00000922697chr12:95905671-95905774104MAP2_HUMAN322-356351A:322-35635
1.10ENST0000032366610ENSE00000922698chr12:95906577-95906692116MAP2_HUMAN357-395391A:357-39539
1.11ENST0000032366611ENSE00001295819chr12:95907428-959096152188MAP2_HUMAN395-478841A:395-47884

(-) 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:355
 aligned with MAP2_HUMAN | P50579 from UniProtKB/Swiss-Prot  Length:478

    Alignment length:369
                                   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       389       399       409       419       429       439       449       459       469         
           MAP2_HUMAN   110 KVQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKALDQASEEIWNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDICKIDFGTHISGRIIDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDGKTYQVKPIRNLNGHSIGQYRIHAGKTVPIVKGGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTILLRPTCKEVVSRGDDY 478
               SCOP domains d2oaza2 A:1-374,A:449-478 Met              hionine aminopeptidase                                                                                                                                                                                                        d2oaza1 A:375-448 Methionine aminopeptidase, insert domain                d2oaza2 A:1-374,A:449-478      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................eee...--------------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh......eeeeeeeeeee..eee.................eeeeeeeee..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee..eeee.ee.....eee..........ee...............eeeeeeeee......ee.....eeee..........hhhhhhhhhhhhhhh....eehhhhhh.....hhhhhhhhhhh..eeee..ee......eeeeeeeeee....eee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------MAP_2            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:1-29 [INCOMPLETE]-----------------------------------------------------Exon 1.6  PDB: A:197-258 UniProt: 197-258                     -------------------------------Exon 1.8  PDB: A:290-322         ----------------------------------Exon 1.10  PDB: A:357-395              ----------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.5  PDB: A:153-197 UniProt: 143-197 [INCOMPLETE] ------------------------------------------------------------Exon 1.7  PDB: A:258-289        --------------------------------Exon 1.9  PDB: A:322-356           --------------------------------------Exon 1.11  PDB: A:395-478 UniProt: 395-478                                           Transcript 1 (2)
                 2oaz A   1 KVQTDPPSVPICDLYPNGVFPKGQECEYP--------------EEKKALDQASEEIWNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDICKIDFGTHISGRIIDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDGKTYQVKPIRNLNGHSIGQYRIHAGKTVPIIKGGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTILLRPTCKEVVSRGDDY 478
                                    10        20        |-         -   |   159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469         
                                                       29            153
   Legend:   → Mismatch (orange background)
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  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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OAZ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MAP2_HUMAN | P50579)
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:0070084    protein initiator methionine removal    The protein modification process in which the translation-initiating methionine or formylmethionine residue is removed from a protein.
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of 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.
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: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.

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 Related Entries

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UniProtKB/Swiss-Prot
        MAP2_HUMAN | P50579: 1b59 1b6a 1bn5 1boa 1kq0 1kq9 1qzy 1r58 1r5g 1r5h 1yw7 1yw8 1yw9 2adu 2ea2 2ea4 2ga2 5cls 5d6e 5d6f 5jfr 5jhu 5ji6

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