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(-) Description

Title :  HUMAN METHIONINE AMINOPEPTIDASE COMPLEX WITH 4-ARYL-1,2,3-TRIAZOLE INHIBITOR
 
Authors :  L. S. Kallander, Q. Lu, W. Chen, T. Tomaszek, G. Yang, D. Tew, T. D. Meek, G. A. Hofmann, C. K. Schulz-Pritchard, W. W. Smith, C. A. Janson, M. D. Ryan, G. F. Zhang, K. O. Johanson, R. B. Kirkpatrick, T. F. Ho, P. W. Fisher, M. R. Mattern, R. K. Johnson, M. J. Hansbury, J. D. Winkler K. W. Ward, D. F. Veber, S. K. Thompson
Date :  20 Jul 05  (Deposition) - 13 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Aminopeptidase, Metal Binding, Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. S. Kallander, Q. Lu, W. Chen, T. Tomaszek, G. Yang, D. Tew, T. D. Meek, G. A. Hofmann, C. K. Schulz-Pritchard, W. W. Smith, C. A. Janson, M. D. Ryan, G. F. Zhang, K. O. Johanson, R. B. Kirkpatrick, T. F. Ho, P. W. Fisher, M. R. Mattern, R. K. Johnson, M. J. Hansbury, J. D. Winkler, K. W. Ward, D. F. Veber, S. K. Thompson
4-Aryl-1, 2, 3-Triazole: A Novel Template For A Reversible Methionine Aminopeptidase 2 Inhibitor, Optimized To Inhibit Angiogenesis In Vivo
J. Med. Chem. V. 48 5644 2005
PubMed-ID: 16134930  |  Reference-DOI: 10.1021/JM050408C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHIONINE AMINOPEPTIDASE 2
    Chains: A
    EC Number: 3.4.11.18
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC-1
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: RESIDUES 110-478
    Gene: METAP2, MNPEP, P67EIF2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: METAP 2, PEPTIDASE M 2, INITIATION FACTOR 2 ASSOCIATED 67 KDA GLYCOPROTEIN, P67, P67EIF2

 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
2R201Ligand/Ion4-(3-METHYLPHENYL)-1H-1,2,3-TRIAZOLE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:251 , ASP A:262 , GLU A:459 , CO A:502 , R20 A:906BINDING SITE FOR RESIDUE CO A 501
2AC2SOFTWAREASP A:262 , HIS A:331 , GLU A:364 , GLU A:459 , CO A:501 , R20 A:906BINDING SITE FOR RESIDUE CO A 502
3AC3SOFTWAREHIS A:231 , ASP A:251 , ASP A:262 , HIS A:331 , HIS A:339 , GLU A:364 , HIS A:382 , TYR A:444 , GLU A:459 , CO A:501 , CO A:502 , HOH A:671BINDING SITE FOR RESIDUE R20 A 906

(-) 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 2ADU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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:110-13829
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 d2adua2 A:110-374,A:449-478 M              ethionine aminopeptidase                                                                                                                                                                                                      d2adua1 A:375-448 Methionine aminopeptidase, insert domain                d2adua2 A:110-374,A:449-478    SCOP domains
               CATH domains ------------------------------------------------------2aduA01 A:164-371,A:451-474 Creatinase/methionine aminopeptidase superfamily                                                                                                                                    2aduA02 A:372-450 'winged helix' repressor DNA binding domain                  2aduA01                 ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh.........eee...--------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.....eeeeeeeeeee..eee.................eeeeeeeee..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee..eeee.ee....eeeee.........eee..............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:110-138          -----------------------------------------------------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)
                 2adu A 110 KVQTDPPSVPICDLYPNGVFPKGQECEYP--------------EEKKALDQASEEIWNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDICKIDFGTHISGRIIDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDGKTYQVKPIRNLNGHSIGQYRIHAGKTVPIIKGGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTILLRPTCKEVVSRGDDY 478
                                   119       129        |-         -   |   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         
                                                      138            153
   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  (2, 2)

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

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) 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

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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

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