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(-) Description

Title :  EXPRESSION, CRYSTALLIZATION AND THREE-DIMENSIONAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN PLASMA KALLIKREIN: IMPLICATIONS FOR STRUCTURE-BASED DESIGN OF PROTEASE INHIBITORS
 
Authors :  J. Tang, C. L. Yu, S. R. Williams, E. Springman, D. Jeffery, P. A. Sprengeler, A. Estevez, J. Sampang, W. Shrader, J. R. Spencer, W. B. Young, M. E. Mcgrath, B. A. Katz
Date :  11 Aug 05  (Deposition) - 11 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Trypsin-Like Serine Protease; Enzymatically Deglycosylated, Blood Clotting, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Tang, C. L. Yu, S. R. Williams, E. Springman, D. Jeffery, P. A. Sprengeler, A. Estevez, J. Sampang, W. Shrader, J. Spencer, W. Young, M. Mcgrath, B. A. Katz
Expression, Crystallization, And Three-Dimensional Structure Of The Catalytic Domain Of Human Plasma Kallikrein.
J. Biol. Chem. V. 280 41077 2005
PubMed-ID: 16199530  |  Reference-DOI: 10.1074/JBC.M506766200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLASMA KALLIKREIN, LIGHT CHAIN
    ChainsA
    EC Number3.4.21.34
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System StrainSF9
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentPROTEASE DOMAIN, ENZYMATICALLY DEGLYCOSYLATED
    GeneKLKB1, KLK3
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymKININOGENIN;
FLETCHER FACTOR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1BAM1Ligand/IonBENZAMIDINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:189 , ALA A:190 , CYS A:191 , LYS A:192 , SER A:195 , TRP A:215 , GLY A:216 , GLY A:219 , CYS A:220 , GLY A:226 , HOH A:269 , HOH A:734 , HOH A:848BINDING SITE FOR RESIDUE BAM A 249

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:58
2A:136 -A:201
3A:168 -A:182
4A:191 -A:220

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016285Q442PKLKB1_HUMANPolymorphism4253316AQ62P
2UniProtVAR_054908C548YKLKB1_HUMANDisease (PKK deficiency)  ---AC168Y
3UniProtVAR_016286R560QKLKB1_HUMANPolymorphism4253325AR179Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLKB1_HUMAN391-626  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLKB1_HUMAN430-435  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLKB1_HUMAN572-583  1A:189-200

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4aENST000002646904aENSE00001941670chr4:187148556-187148741186KLKB1_HUMAN-00--
1.5aENST000002646905aENSE00002195944chr4:187149349-18714940759KLKB1_HUMAN1-20200--
1.7ENST000002646907ENSE00001775846chr4:187153281-187153443163KLKB1_HUMAN20-74550--
1.8ENST000002646908ENSE00001083696chr4:187155106-187155212107KLKB1_HUMAN74-110370--
1.9cENST000002646909cENSE00001169305chr4:187157935-187158094160KLKB1_HUMAN110-163540--
1.10bENST0000026469010bENSE00000970679chr4:187159410-187159519110KLKB1_HUMAN163-200380--
1.11aENST0000026469011aENSE00001505207chr4:187171397-187171556160KLKB1_HUMAN200-253540--
1.12bENST0000026469012bENSE00000886908chr4:187172373-187172482110KLKB1_HUMAN253-290380--
1.13ENST0000026469013ENSE00000886909chr4:187172641-187172803163KLKB1_HUMAN290-344550--
1.14ENST0000026469014ENSE00000886910chr4:187172903-187173015113KLKB1_HUMAN344-382390--
1.15bENST0000026469015bENSE00000886911chr4:187173171-187173339169KLKB1_HUMAN382-438571A:16-60A48
1.16ENST0000026469016ENSE00000886912chr4:187175742-187175917176KLKB1_HUMAN438-497601A:60A-116 (gaps)62
1.17ENST0000026469017ENSE00001198620chr4:187177146-18717724196KLKB1_HUMAN497-529331A:116-14833
1.18ENST0000026469018ENSE00001198616chr4:187178380-187178519140KLKB1_HUMAN529-575471A:148-192 (gaps)50
1.19dENST0000026469019dENSE00001612709chr4:187179175-187179625451KLKB1_HUMAN576-638631A:193-245 (gaps)56

(-) 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:238
 aligned with KLKB1_HUMAN | P03952 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:238
                                   400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620        
         KLKB1_HUMAN    391 IVGGTNSSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILNLSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLNYTEFQKPICLPSKGDTSTIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGGKDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQSS  628
               SCOP domains d2anwa_ A: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2anwA01     2anwA02 A:28-120,A:234-245 Trypsin-like serine proteases                                           2anwA01 A:16-27,A:121-233 Trypsin-like serine proteases                                                            2anwA02      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeeee...eeeeeeeeeee..eeeehhhhhh...hhh.eeeee...hhhhh........eeeeee.............eeeee................hhhhhhh....eeeee..............eeeee.eehhhhhhhhh........eeee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------P---------------------------------------------------------------------------------------------------------Y-----------Q-------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 391-626                                                                                                                                                                                                 -- PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.15b  PDB: A:16-60A UniProt: 382-438      ----------------------------------------------------------Exon 1.17  PDB: A:116-148        ----------------------------------------------Exon 1.19d  PDB: A:193-245 (gaps) UniProt: 576-638    Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.16  PDB: A:60A-116 (gaps) UniProt: 438-497           -------------------------------Exon 1.18  PDB: A:148-192 (gaps)               ----------------------------------------------------- Transcript 1 (2)
                2anw A   16 IVGGTNSSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILNLSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLNYTEFQKPISLPSKGDTSTIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGGKDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQSS  245
                                    25        35   ||   43        53       60C |||||  69        79        89        99       109       119       129       139       150       160       170   |   179     |186B||     197      208C|      217|  |   227       237        
                                                 38A|                    60A|| |||||                                                                                148|                    173A        184A  ||||             205|||      217|  |                        
                                                  38B                     60B| |||||                                                                                 150                                   186A|||             208B||       219  |                        
                                                                           60C |||||                                                                                                                        186B||              208C|         221A                        
                                                                              62||||                                                                                                                         186C|               208D                                     
                                                                              65B|||                                                                                                                           189                                                        
                                                                               65C||                                                                                                                                                                                      
                                                                                65D|                                                                                                                                                                                      
                                                                                 65E                                                                                                                                                                                      

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KLKB1_HUMAN | P03952)
molecular function
    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: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.
    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).
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0002542    Factor XII activation    Any process that activates Factor XII (Hageman factor). Factor XII is a protein synthesized by the liver that circulates in an inactive form until it encounters collagen or basement membrane or activated platelets (as occurs at the site of endothelial injury). Factor XII then undergoes a conformational change (becoming factor XIIa), exposing an active serine center that can subsequently cleave protein substrates and activate a variety of mediator systems. Factor XII is a participant in the clotting cascade as well as the kinin cascade.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0007597    blood coagulation, intrinsic pathway    A protein activation cascade that contributes to blood coagulation and consists of the interactions among high molecular weight kininogen, prekallikrein, and factor XII that lead to the activation of clotting factor X.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0097421    liver regeneration    The regrowth of lost or destroyed liver.
    GO:0031639    plasminogen activation    The process in which inactive plasminogen is processed to active plasmin. This process includes cleavage at an internal Arg-Val site to form an N-terminal A-chain and C-terminal B-chain held together by a disulfide bond, and can include further proteolytic cleavage events to remove the preactivation peptide.
    GO:0051919    positive regulation of fibrinolysis    Any process that activates, maintains or increases the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0031638    zymogen activation    The proteolytic processing of an inactive enzyme to an active form.
cellular component
    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: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
        KLKB1_HUMAN | P039522any 4ogx 4ogy 5f8t 5f8x 5f8z 5tjx

(-) Related Entries Specified in the PDB File

2any MUTAGENICALLY DEGLYCOSYLATED COUNTERPART OF ENZYMATICALLY DEGLYCOSYLATED HUMAN PLASMA KALLIKREIN PROTEASE DOMAIN,