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(-) Description

Title :  A HIGH RESOLUTION STRUCTURE OF HUMAN GLUTAMATE CARBOXYPEPTIDASE II (GCPII) IN COMPLEX WITH FOLYLDI-GAMMA-L-GLUTAMIC ACID (PTEROYLTRI-GAMMA-L-GLUTAMIC ACID)
 
Authors :  M. Navratil, C. Barinka
Date :  21 Aug 13  (Deposition) - 18 Jun 14  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Metallopeptidase, Hydrolase-Hydrolase Inhibitor Complex, Prostate Specific Membrane Antigen, Folate Hydrolase 1, Folh1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Navratil, J. Ptacek, P. Sacha, J. Starkova, J. Lubkowski, C. Barinka, J. Konvalinka
Structural And Biochemical Characterization Of The Folyl-Poly-Gamma-L-Glutamate Hydrolyzing Activity Of Human Glutamate Carboxypeptidase Ii.
Febs J. V. 281 3228 2014
PubMed-ID: 24863754  |  Reference-DOI: 10.1111/FEBS.12857

(-) Compounds

Molecule 1 - GLUTAMATE CARBOXYPEPTIDASE 2
    Chains: A
    EC Number: 3.4.17.21
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Cell Line: SCHNEIDER'S S2
    Expression System Taxid: 7227
    Fragment: GLUTAMATE CARBOXYPEPTIDASE II, UNP RESIDUES 44-750
    Gene: FOLH1, FOLH, NAALAD1, PSM, PSMA, GIG27
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CELL GROWTH-INHIBITING GENE 27 PROTEIN, FOLATE HYDROLASE 1, FOLYLPOLY-GAMMA-GLUTAMATE CARBOXYPEPTIDASE, FGCP, GLUTAMATE CARBOXYPEPTIDASE II, GCPII, MEMBRANE GLUTAMATE CARBOXYPEPTIDASE, MGCP, N-ACETYLATED-ALPHA-LINKED ACIDIC DIPEPTIDASE I, NAALADASE I, PROSTATE-SPECIFIC MEMBRANE ANTIGEN, PSM, PSMA, PTEROYLPOLY-GAMMA- GLUTAMATE CARBOXYPEPTIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 18)

Asymmetric Unit (7, 18)
No.NameCountTypeFull Name
129C1Ligand/IonN-(4-{[(2-AMINO-4-OXO-3,4-DIHYDROPTERIDIN-6-YL)METHYL]AMINO}BENZOYL)-L-GAMMA-GLUTAMYL-L-GAMMA-GLUTAMYL-L-GLUTAMIC ACID
2BMA1Ligand/IonBETA-D-MANNOSE
3CA1Ligand/IonCALCIUM ION
4CL1Ligand/IonCHLORIDE ION
5MAN1Ligand/IonALPHA-D-MANNOSE
6NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
7ZN2Ligand/IonZINC ION
Biological Unit 1 (4, 28)
No.NameCountTypeFull Name
129C2Ligand/IonN-(4-{[(2-AMINO-4-OXO-3,4-DIHYDROPTERIDIN-6-YL)METHYL]AMINO}BENZOYL)-L-GAMMA-GLUTAMYL-L-GAMMA-GLUTAMYL-L-GLUTAMIC ACID
2BMA2Ligand/IonBETA-D-MANNOSE
3CA-1Ligand/IonCALCIUM ION
4CL-1Ligand/IonCHLORIDE ION
5MAN2Ligand/IonALPHA-D-MANNOSE
6NAG22Ligand/IonN-ACETYL-D-GLUCOSAMINE
7ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:387 , GLU A:425 , HIS A:553 , ZN A:802 , 29C A:818 , HOH A:1309BINDING SITE FOR RESIDUE ZN A 801
02AC2SOFTWAREHIS A:377 , ASP A:387 , GLU A:425 , ASP A:453 , ZN A:801 , HOH A:1309BINDING SITE FOR RESIDUE ZN A 802
03AC3SOFTWARETHR A:269 , TYR A:272 , GLU A:433 , GLU A:436 , HOH A:906BINDING SITE FOR RESIDUE CA A 803
04AC4SOFTWAREASN A:451 , ASP A:453 , ARG A:534 , ARG A:536 , HOH A:921BINDING SITE FOR RESIDUE CL A 804
05AC5SOFTWAREASN A:76 , GLN A:95 , GLN A:99 , NAG A:806 , HOH A:1124 , HOH A:1255BINDING SITE FOR RESIDUE NAG A 805
06AC6SOFTWARENAG A:805BINDING SITE FOR RESIDUE NAG A 806
07AC7SOFTWAREASN A:121 , HIS A:124 , THR A:349 , HOH A:1100BINDING SITE FOR RESIDUE NAG A 807
08AC8SOFTWARETYR A:127 , GLU A:137 , ILE A:138 , ASN A:140 , NAG A:809BINDING SITE FOR RESIDUE NAG A 808
09AC9SOFTWARENAG A:808 , HOH A:1342BINDING SITE FOR RESIDUE NAG A 809
10BC1SOFTWAREASN A:195 , SER A:197BINDING SITE FOR RESIDUE NAG A 810
11BC2SOFTWARETRP A:246 , ASN A:459 , PHE A:565 , TYR A:566 , HOH A:978 , HOH A:1140 , HOH A:1299 , HOH A:1322 , HOH A:1374BINDING SITE FOR RESIDUE NAG A 811
12BC3SOFTWARESER A:472 , ASN A:476 , PRO A:594 , NAG A:813 , HOH A:1406 , HOH A:1420BINDING SITE FOR RESIDUE NAG A 812
13BC4SOFTWAREGLN A:651 , NAG A:812 , HOH A:1262BINDING SITE FOR RESIDUE NAG A 813
14BC5SOFTWARETYR A:277 , SER A:631 , SER A:634 , ASN A:638 , GLN A:740 , NAG A:815 , HOH A:1024 , HOH A:1057 , HOH A:1183BINDING SITE FOR RESIDUE NAG A 814
15BC6SOFTWAREGLU A:276 , NAG A:814 , BMA A:816BINDING SITE FOR RESIDUE NAG A 815
16BC7SOFTWAREHIS A:112 , GLU A:276 , ARG A:354 , NAG A:815 , MAN A:817BINDING SITE FOR RESIDUE BMA A 816
17BC8SOFTWAREPHE A:235 , LYS A:240 , SER A:241 , GLU A:276 , ARG A:354 , BMA A:816 , HOH A:1261 , HOH A:1277BINDING SITE FOR RESIDUE MAN A 817
18BC9SOFTWARELYS A:207 , ARG A:210 , ASN A:257 , ASP A:387 , ALA A:424 , GLU A:425 , GLY A:427 , ARG A:463 , ARG A:511 , GLY A:518 , ASN A:519 , ARG A:534 , ARG A:536 , TRP A:541 , GLU A:542 , TYR A:552 , HIS A:553 , ASN A:698 , LYS A:699 , TYR A:700 , ZN A:801 , HOH A:909 , HOH A:1060 , HOH A:1067 , HOH A:1260 , HOH A:1268 , HOH A:1276 , HOH A:1309 , HOH A:1373 , HOH A:1415BINDING SITE FOR RESIDUE 29C A 818

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MCQ)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Tyr A:242 -Pro A:243
2Gly A:330 -Pro A:331
3Asp A:387 -Pro A:388

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MCQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MCQ)

(-) Exons   (0, 0)

(no "Exon" information available for 4MCQ)

(-) Sequences/Alignments

Asymmetric 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:693
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...eeeeeeeeeeeee.......eeeee.....eeee.....................ee.......ee.eee....hhhhhhhhhhh........eeeee....hhhhhhhhhhhh...eeeee.hhhhhh....................ee........................hhhhh.......eeeehhhhhhhhhh........hhhhh.............hhhhh..eeeee...eeeeeeeeeeeeee....eeeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhh.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhheeeeee.........eeeeee...hhhhhhhhhhh...........hhhhhhhhhh...................hhhhhhh...eeeeeeee...................hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh................eeee..eeeeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mcq A  56 HNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFGLDSVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYENVSDIVPPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQKLLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTRIYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVRSFGTLKKEGWRPRRTILFASWDAAEFGLLGSTEWAEENSRLLQERGVAYINADSSIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSPEFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETNKFSGYPLYHSVYETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFSNPIVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA 750
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       657       667       677       687       697       707       717       727       737       747   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               653|                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                656
   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  (0, 0)

(no "SCOP Domain" information available for 4MCQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MCQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MCQ)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        FOLH1_HUMAN | Q04609: 1z8l 2c6c 2c6g 2c6p 2cij 2jbj 2jbk 2oot 2or4 2pvv 2pvw 2xef 2xeg 2xei 2xej 3bhx 3bi0 3bi1 3bxm 3d7d 3d7f 3d7g 3d7h 3iww 3rbu 3sje 3sjf 3sjg 3sjx 4jyw 4jz0 4lqg 4mcp 4mcr 4mcs 4ngm 4ngn 4ngp 4ngq 4ngr 4ngs 4ngt 4oc0 4oc1 4oc2 4oc3 4oc4 4oc5 4ome 4p44 4p45 4p4b 4p4d 4p4e 4p4f 4p4i 4p4j 4w9y 4x3r 5d29 5ely 5f09

(-) Related Entries Specified in the PDB File

4mcp 4mcr 4mcs